Starting phenix.real_space_refine on Mon Oct 14 20:14:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juu_36664/10_2024/8juu_36664.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juu_36664/10_2024/8juu_36664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juu_36664/10_2024/8juu_36664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juu_36664/10_2024/8juu_36664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juu_36664/10_2024/8juu_36664.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juu_36664/10_2024/8juu_36664.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 88 9.91 5 Ni 2 6.56 5 S 752 5.16 5 C 42926 2.51 5 N 12106 2.21 5 O 14144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 489 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 70018 Number of models: 1 Model: "" Number of chains: 62 Chain: "A" Number of atoms: 33638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4308, 33638 Classifications: {'peptide': 4308} Link IDs: {'PCIS': 1, 'PTRANS': 211, 'TRANS': 4095} Chain breaks: 1 Chain: "B" Number of atoms: 33638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4308, 33638 Classifications: {'peptide': 4308} Link IDs: {'PCIS': 1, 'PTRANS': 211, 'TRANS': 4095} Chain breaks: 1 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 33 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 33 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "2" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 367 Unusual residues: {' CA': 44, ' NI': 1, 'A2G': 11, 'NAG': 12} Classifications: {'undetermined': 68} Link IDs: {None: 67} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 23 Chain: "B" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 367 Unusual residues: {' CA': 44, ' NI': 1, 'A2G': 11, 'NAG': 12} Classifications: {'undetermined': 68} Link IDs: {None: 67} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 23 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 67430 SG CYS J 2 73.814 139.642 250.686 1.00123.16 S ATOM 67320 SG CYS D 2 94.579 143.722 251.359 1.00117.01 S Time building chain proxies: 30.40, per 1000 atoms: 0.43 Number of scatterers: 70018 At special positions: 0 Unit cell: (173.553, 283.611, 286.433, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 2 28.00 Ca 88 19.99 S 752 16.00 O 14144 8.00 N 12106 7.00 C 42926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=305, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 40 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.02 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 62 " distance=2.02 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 80 " distance=2.04 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 93 " distance=2.04 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 103 " distance=2.04 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 222 " - pdb=" SG CYS A 234 " distance=2.04 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 256 " distance=2.04 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 278 " distance=2.04 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 351 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 357 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 384 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 673 " distance=2.04 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 688 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 703 " distance=2.03 Simple disulfide: pdb=" SG CYS A 973 " - pdb=" SG CYS A 987 " distance=2.03 Simple disulfide: pdb=" SG CYS A 983 " - pdb=" SG CYS A 997 " distance=2.03 Simple disulfide: pdb=" SG CYS A 999 " - pdb=" SG CYS A1012 " distance=2.05 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1037 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1050 " distance=2.04 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1059 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1079 " distance=2.02 Simple disulfide: pdb=" SG CYS A1073 " - pdb=" SG CYS A1092 " distance=2.04 Simple disulfide: pdb=" SG CYS A1086 " - pdb=" SG CYS A1101 " distance=2.03 Simple disulfide: pdb=" SG CYS A1110 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS A1117 " - pdb=" SG CYS A1135 " distance=2.03 Simple disulfide: pdb=" SG CYS A1129 " - pdb=" SG CYS A1144 " distance=2.04 Simple disulfide: pdb=" SG CYS A1150 " - pdb=" SG CYS A1162 " distance=2.03 Simple disulfide: pdb=" SG CYS A1157 " - pdb=" SG CYS A1175 " distance=2.04 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1184 " distance=2.03 Simple disulfide: pdb=" SG CYS A1188 " - pdb=" SG CYS A1201 " distance=2.03 Simple disulfide: pdb=" SG CYS A1195 " - pdb=" SG CYS A1214 " distance=2.03 Simple disulfide: pdb=" SG CYS A1208 " - pdb=" SG CYS A1223 " distance=2.04 Simple disulfide: pdb=" SG CYS A1231 " - pdb=" SG CYS A1244 " distance=2.03 Simple disulfide: pdb=" SG CYS A1238 " - pdb=" SG CYS A1257 " distance=2.02 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1267 " distance=2.03 Simple disulfide: pdb=" SG CYS A1272 " - pdb=" SG CYS A1284 " distance=2.03 Simple disulfide: pdb=" SG CYS A1279 " - pdb=" SG CYS A1297 " distance=2.03 Simple disulfide: pdb=" SG CYS A1291 " - pdb=" SG CYS A1306 " distance=2.02 Simple disulfide: pdb=" SG CYS A1313 " - pdb=" SG CYS A1326 " distance=2.03 Simple disulfide: pdb=" SG CYS A1320 " - pdb=" SG CYS A1339 " distance=2.03 Simple disulfide: pdb=" SG CYS A1333 " - pdb=" SG CYS A1349 " distance=2.04 Simple disulfide: pdb=" SG CYS A1354 " - pdb=" SG CYS A1365 " distance=2.04 Simple disulfide: pdb=" SG CYS A1361 " - pdb=" SG CYS A1374 " distance=2.02 Simple disulfide: pdb=" SG CYS A1376 " - pdb=" SG CYS A1389 " distance=2.03 Simple disulfide: pdb=" SG CYS A1395 " - pdb=" SG CYS A1405 " distance=2.03 Simple disulfide: pdb=" SG CYS A1401 " - pdb=" SG CYS A1414 " distance=2.04 Simple disulfide: pdb=" SG CYS A1416 " - pdb=" SG CYS A1429 " distance=2.04 Simple disulfide: pdb=" SG CYS A1710 " - pdb=" SG CYS A1726 " distance=2.04 Simple disulfide: pdb=" SG CYS A1728 " - pdb=" SG CYS A1741 " distance=2.03 Simple disulfide: pdb=" SG CYS A2023 " - pdb=" SG CYS A2034 " distance=2.04 Simple disulfide: pdb=" SG CYS A2030 " - pdb=" SG CYS A2044 " distance=2.03 Simple disulfide: pdb=" SG CYS A2046 " - pdb=" SG CYS A2059 " distance=2.03 Simple disulfide: pdb=" SG CYS A2347 " - pdb=" SG CYS A2358 " distance=2.04 Simple disulfide: pdb=" SG CYS A2354 " - pdb=" SG CYS A2369 " distance=2.03 Simple disulfide: pdb=" SG CYS A2371 " - pdb=" SG CYS A2383 " distance=2.03 Simple disulfide: pdb=" SG CYS A2518 " - pdb=" SG CYS A2652 " distance=2.04 Simple disulfide: pdb=" SG CYS A2656 " - pdb=" SG CYS A2667 " distance=2.03 Simple disulfide: pdb=" SG CYS A2663 " - pdb=" SG CYS A2676 " distance=2.01 Simple disulfide: pdb=" SG CYS A2678 " - pdb=" SG CYS A2693 " distance=2.03 Simple disulfide: pdb=" SG CYS A2701 " - pdb=" SG CYS A2713 " distance=2.03 Simple disulfide: pdb=" SG CYS A2708 " - pdb=" SG CYS A2726 " distance=2.03 Simple disulfide: pdb=" SG CYS A2720 " - pdb=" SG CYS A2737 " distance=2.03 Simple disulfide: pdb=" SG CYS A2742 " - pdb=" SG CYS A2754 " distance=2.03 Simple disulfide: pdb=" SG CYS A2749 " - pdb=" SG CYS A2767 " distance=2.03 Simple disulfide: pdb=" SG CYS A2761 " - pdb=" SG CYS A2776 " distance=2.03 Simple disulfide: pdb=" SG CYS A2781 " - pdb=" SG CYS A2794 " distance=2.01 Simple disulfide: pdb=" SG CYS A2789 " - pdb=" SG CYS A2807 " distance=2.04 Simple disulfide: pdb=" SG CYS A2801 " - pdb=" SG CYS A2818 " distance=2.03 Simple disulfide: pdb=" SG CYS A2823 " - pdb=" SG CYS A2836 " distance=2.04 Simple disulfide: pdb=" SG CYS A2830 " - pdb=" SG CYS A2849 " distance=2.05 Simple disulfide: pdb=" SG CYS A2843 " - pdb=" SG CYS A2860 " distance=2.04 Simple disulfide: pdb=" SG CYS A2865 " - pdb=" SG CYS A2878 " distance=2.03 Simple disulfide: pdb=" SG CYS A2872 " - pdb=" SG CYS A2891 " distance=2.03 Simple disulfide: pdb=" SG CYS A2885 " - pdb=" SG CYS A2901 " distance=2.05 Simple disulfide: pdb=" SG CYS A2908 " - pdb=" SG CYS A2920 " distance=2.05 Simple disulfide: pdb=" SG CYS A2915 " - pdb=" SG CYS A2933 " distance=2.02 Simple disulfide: pdb=" SG CYS A2927 " - pdb=" SG CYS A2945 " distance=2.03 Simple disulfide: pdb=" SG CYS A2950 " - pdb=" SG CYS A2967 " distance=2.03 Simple disulfide: pdb=" SG CYS A2957 " - pdb=" SG CYS A2980 " distance=2.04 Simple disulfide: pdb=" SG CYS A2974 " - pdb=" SG CYS A2990 " distance=2.03 Simple disulfide: pdb=" SG CYS A2995 " - pdb=" SG CYS A3007 " distance=2.03 Simple disulfide: pdb=" SG CYS A3002 " - pdb=" SG CYS A3020 " distance=2.03 Simple disulfide: pdb=" SG CYS A3014 " - pdb=" SG CYS A3029 " distance=2.04 Simple disulfide: pdb=" SG CYS A3034 " - pdb=" SG CYS A3046 " distance=2.03 Simple disulfide: pdb=" SG CYS A3041 " - pdb=" SG CYS A3059 " distance=2.04 Simple disulfide: pdb=" SG CYS A3053 " - pdb=" SG CYS A3070 " distance=2.03 Simple disulfide: pdb=" SG CYS A3077 " - pdb=" SG CYS A3089 " distance=2.03 Simple disulfide: pdb=" SG CYS A3084 " - pdb=" SG CYS A3102 " distance=2.02 Simple disulfide: pdb=" SG CYS A3096 " - pdb=" SG CYS A3111 " distance=2.03 Simple disulfide: pdb=" SG CYS A3116 " - pdb=" SG CYS A3128 " distance=2.04 Simple disulfide: pdb=" SG CYS A3124 " - pdb=" SG CYS A3137 " distance=2.03 Simple disulfide: pdb=" SG CYS A3139 " - pdb=" SG CYS A3152 " distance=2.03 Simple disulfide: pdb=" SG CYS A3158 " - pdb=" SG CYS A3169 " distance=2.02 Simple disulfide: pdb=" SG CYS A3165 " - pdb=" SG CYS A3178 " distance=2.03 Simple disulfide: pdb=" SG CYS A3180 " - pdb=" SG CYS A3193 " distance=2.04 Simple disulfide: pdb=" SG CYS A3313 " - pdb=" SG CYS A3321 " distance=2.05 Simple disulfide: pdb=" SG CYS A3471 " - pdb=" SG CYS A3482 " distance=2.04 Simple disulfide: pdb=" SG CYS A3478 " - pdb=" SG CYS A3493 " distance=2.04 Simple disulfide: pdb=" SG CYS A3495 " - pdb=" SG CYS A3510 " distance=2.03 Simple disulfide: pdb=" SG CYS A3514 " - pdb=" SG CYS A3527 " distance=2.04 Simple disulfide: pdb=" SG CYS A3521 " - pdb=" SG CYS A3540 " distance=2.03 Simple disulfide: pdb=" SG CYS A3534 " - pdb=" SG CYS A3550 " distance=2.03 Simple disulfide: pdb=" SG CYS A3555 " - pdb=" SG CYS A3567 " distance=2.03 Simple disulfide: pdb=" SG CYS A3562 " - pdb=" SG CYS A3580 " distance=2.04 Simple disulfide: pdb=" SG CYS A3574 " - pdb=" SG CYS A3591 " distance=2.04 Simple disulfide: pdb=" SG CYS A3596 " - pdb=" SG CYS A3608 " distance=2.04 Simple disulfide: pdb=" SG CYS A3603 " - pdb=" SG CYS A3621 " distance=2.04 Simple disulfide: pdb=" SG CYS A3615 " - pdb=" SG CYS A3632 " distance=2.04 Simple disulfide: pdb=" SG CYS A3637 " - pdb=" SG CYS A3649 " distance=2.03 Simple disulfide: pdb=" SG CYS A3644 " - pdb=" SG CYS A3662 " distance=2.03 Simple disulfide: pdb=" SG CYS A3656 " - pdb=" SG CYS A3673 " distance=2.03 Simple disulfide: pdb=" SG CYS A3680 " - pdb=" SG CYS A3694 " distance=2.03 Simple disulfide: pdb=" SG CYS A3688 " - pdb=" SG CYS A3707 " distance=2.04 Simple disulfide: pdb=" SG CYS A3701 " - pdb=" SG CYS A3716 " distance=2.03 Simple disulfide: pdb=" SG CYS A3721 " - pdb=" SG CYS A3734 " distance=2.04 Simple disulfide: pdb=" SG CYS A3729 " - pdb=" SG CYS A3747 " distance=2.04 Simple disulfide: pdb=" SG CYS A3741 " - pdb=" SG CYS A3756 " distance=2.04 Simple disulfide: pdb=" SG CYS A3761 " - pdb=" SG CYS A3773 " distance=2.04 Simple disulfide: pdb=" SG CYS A3768 " - pdb=" SG CYS A3786 " distance=2.04 Simple disulfide: pdb=" SG CYS A3780 " - pdb=" SG CYS A3795 " distance=2.03 Simple disulfide: pdb=" SG CYS A3800 " - pdb=" SG CYS A3812 " distance=2.04 Simple disulfide: pdb=" SG CYS A3807 " - pdb=" SG CYS A3825 " distance=2.04 Simple disulfide: pdb=" SG CYS A3819 " - pdb=" SG CYS A3834 " distance=2.03 Simple disulfide: pdb=" SG CYS A3844 " - pdb=" SG CYS A3856 " distance=2.03 Simple disulfide: pdb=" SG CYS A3851 " - pdb=" SG CYS A3869 " distance=2.05 Simple disulfide: pdb=" SG CYS A3863 " - pdb=" SG CYS A3880 " distance=2.04 Simple disulfide: pdb=" SG CYS A3885 " - pdb=" SG CYS A3898 " distance=2.04 Simple disulfide: pdb=" SG CYS A3893 " - pdb=" SG CYS A3911 " distance=2.02 Simple disulfide: pdb=" SG CYS A3905 " - pdb=" SG CYS A3922 " distance=2.04 Simple disulfide: pdb=" SG CYS A3930 " - pdb=" SG CYS A3942 " distance=2.03 Simple disulfide: pdb=" SG CYS A3937 " - pdb=" SG CYS A3955 " distance=2.03 Simple disulfide: pdb=" SG CYS A3949 " - pdb=" SG CYS A3964 " distance=2.03 Simple disulfide: pdb=" SG CYS A3972 " - pdb=" SG CYS A3981 " distance=2.03 Simple disulfide: pdb=" SG CYS A3977 " - pdb=" SG CYS A3991 " distance=2.03 Simple disulfide: pdb=" SG CYS A3993 " - pdb=" SG CYS A4007 " distance=2.03 Simple disulfide: pdb=" SG CYS A4013 " - pdb=" SG CYS A4023 " distance=2.04 Simple disulfide: pdb=" SG CYS A4019 " - pdb=" SG CYS A4032 " distance=2.04 Simple disulfide: pdb=" SG CYS A4034 " - pdb=" SG CYS A4049 " distance=2.03 Simple disulfide: pdb=" SG CYS A4336 " - pdb=" SG CYS A4344 " distance=2.04 Simple disulfide: pdb=" SG CYS A4340 " - pdb=" SG CYS A4353 " distance=2.04 Simple disulfide: pdb=" SG CYS A4355 " - pdb=" SG CYS A4369 " distance=2.03 Simple disulfide: pdb=" SG CYS A4383 " - pdb=" SG CYS A4391 " distance=2.04 Simple disulfide: pdb=" SG CYS A4385 " - pdb=" SG CYS A4401 " distance=2.04 Simple disulfide: pdb=" SG CYS A4403 " - pdb=" SG CYS A4412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 53 " distance=2.04 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 62 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 103 " distance=2.04 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 208 " distance=2.04 Simple disulfide: pdb=" SG CYS B 202 " - pdb=" SG CYS B 217 " distance=2.02 Simple disulfide: pdb=" SG CYS B 222 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 229 " - pdb=" SG CYS B 247 " distance=2.02 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 278 " distance=2.04 Simple disulfide: pdb=" SG CYS B 272 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 306 " distance=2.05 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 316 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 345 " distance=2.04 Simple disulfide: pdb=" SG CYS B 351 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 357 " - pdb=" SG CYS B 370 " distance=2.04 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 384 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 673 " distance=2.06 Simple disulfide: pdb=" SG CYS B 669 " - pdb=" SG CYS B 688 " distance=2.04 Simple disulfide: pdb=" SG CYS B 690 " - pdb=" SG CYS B 703 " distance=2.05 Simple disulfide: pdb=" SG CYS B 973 " - pdb=" SG CYS B 987 " distance=2.03 Simple disulfide: pdb=" SG CYS B 983 " - pdb=" SG CYS B 997 " distance=2.01 Simple disulfide: pdb=" SG CYS B 999 " - pdb=" SG CYS B1012 " distance=2.07 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1037 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1050 " distance=2.03 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1059 " distance=2.04 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1079 " distance=2.04 Simple disulfide: pdb=" SG CYS B1073 " - pdb=" SG CYS B1092 " distance=2.04 Simple disulfide: pdb=" SG CYS B1086 " - pdb=" SG CYS B1101 " distance=2.03 Simple disulfide: pdb=" SG CYS B1110 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B1117 " - pdb=" SG CYS B1135 " distance=2.04 Simple disulfide: pdb=" SG CYS B1129 " - pdb=" SG CYS B1144 " distance=2.04 Simple disulfide: pdb=" SG CYS B1157 " - pdb=" SG CYS B1175 " distance=2.04 Simple disulfide: pdb=" SG CYS B1169 " - pdb=" SG CYS B1184 " distance=2.04 Simple disulfide: pdb=" SG CYS B1188 " - pdb=" SG CYS B1201 " distance=2.04 Simple disulfide: pdb=" SG CYS B1195 " - pdb=" SG CYS B1214 " distance=2.05 Simple disulfide: pdb=" SG CYS B1208 " - pdb=" SG CYS B1223 " distance=2.04 Simple disulfide: pdb=" SG CYS B1231 " - pdb=" SG CYS B1244 " distance=2.03 Simple disulfide: pdb=" SG CYS B1238 " - pdb=" SG CYS B1257 " distance=2.03 Simple disulfide: pdb=" SG CYS B1251 " - pdb=" SG CYS B1267 " distance=2.02 Simple disulfide: pdb=" SG CYS B1272 " - pdb=" SG CYS B1284 " distance=2.02 Simple disulfide: pdb=" SG CYS B1279 " - pdb=" SG CYS B1297 " distance=2.01 Simple disulfide: pdb=" SG CYS B1291 " - pdb=" SG CYS B1306 " distance=2.02 Simple disulfide: pdb=" SG CYS B1313 " - pdb=" SG CYS B1326 " distance=2.04 Simple disulfide: pdb=" SG CYS B1320 " - pdb=" SG CYS B1339 " distance=2.04 Simple disulfide: pdb=" SG CYS B1333 " - pdb=" SG CYS B1349 " distance=2.03 Simple disulfide: pdb=" SG CYS B1354 " - pdb=" SG CYS B1365 " distance=2.04 Simple disulfide: pdb=" SG CYS B1361 " - pdb=" SG CYS B1374 " distance=2.04 Simple disulfide: pdb=" SG CYS B1376 " - pdb=" SG CYS B1389 " distance=2.03 Simple disulfide: pdb=" SG CYS B1395 " - pdb=" SG CYS B1405 " distance=2.04 Simple disulfide: pdb=" SG CYS B1401 " - pdb=" SG CYS B1414 " distance=2.04 Simple disulfide: pdb=" SG CYS B1416 " - pdb=" SG CYS B1429 " distance=2.04 Simple disulfide: pdb=" SG CYS B1705 " - pdb=" SG CYS B1714 " distance=2.05 Simple disulfide: pdb=" SG CYS B1710 " - pdb=" SG CYS B1726 " distance=2.04 Simple disulfide: pdb=" SG CYS B1728 " - pdb=" SG CYS B1741 " distance=2.04 Simple disulfide: pdb=" SG CYS B2023 " - pdb=" SG CYS B2034 " distance=2.04 Simple disulfide: pdb=" SG CYS B2030 " - pdb=" SG CYS B2044 " distance=2.04 Simple disulfide: pdb=" SG CYS B2046 " - pdb=" SG CYS B2059 " distance=2.04 Simple disulfide: pdb=" SG CYS B2347 " - pdb=" SG CYS B2358 " distance=2.04 Simple disulfide: pdb=" SG CYS B2354 " - pdb=" SG CYS B2369 " distance=2.03 Simple disulfide: pdb=" SG CYS B2371 " - pdb=" SG CYS B2383 " distance=2.04 Simple disulfide: pdb=" SG CYS B2518 " - pdb=" SG CYS B2652 " distance=2.04 Simple disulfide: pdb=" SG CYS B2656 " - pdb=" SG CYS B2667 " distance=2.03 Simple disulfide: pdb=" SG CYS B2663 " - pdb=" SG CYS B2676 " distance=2.02 Simple disulfide: pdb=" SG CYS B2678 " - pdb=" SG CYS B2693 " distance=2.04 Simple disulfide: pdb=" SG CYS B2701 " - pdb=" SG CYS B2713 " distance=2.04 Simple disulfide: pdb=" SG CYS B2708 " - pdb=" SG CYS B2726 " distance=2.02 Simple disulfide: pdb=" SG CYS B2720 " - pdb=" SG CYS B2737 " distance=2.04 Simple disulfide: pdb=" SG CYS B2742 " - pdb=" SG CYS B2754 " distance=2.03 Simple disulfide: pdb=" SG CYS B2749 " - pdb=" SG CYS B2767 " distance=2.03 Simple disulfide: pdb=" SG CYS B2761 " - pdb=" SG CYS B2776 " distance=2.03 Simple disulfide: pdb=" SG CYS B2781 " - pdb=" SG CYS B2794 " distance=2.03 Simple disulfide: pdb=" SG CYS B2789 " - pdb=" SG CYS B2807 " distance=2.04 Simple disulfide: pdb=" SG CYS B2801 " - pdb=" SG CYS B2818 " distance=2.04 Simple disulfide: pdb=" SG CYS B2823 " - pdb=" SG CYS B2836 " distance=2.03 Simple disulfide: pdb=" SG CYS B2830 " - pdb=" SG CYS B2849 " distance=2.05 Simple disulfide: pdb=" SG CYS B2843 " - pdb=" SG CYS B2860 " distance=2.04 Simple disulfide: pdb=" SG CYS B2865 " - pdb=" SG CYS B2878 " distance=2.04 Simple disulfide: pdb=" SG CYS B2872 " - pdb=" SG CYS B2891 " distance=2.02 Simple disulfide: pdb=" SG CYS B2885 " - pdb=" SG CYS B2901 " distance=2.04 Simple disulfide: pdb=" SG CYS B2908 " - pdb=" SG CYS B2920 " distance=2.04 Simple disulfide: pdb=" SG CYS B2915 " - pdb=" SG CYS B2933 " distance=2.04 Simple disulfide: pdb=" SG CYS B2927 " - pdb=" SG CYS B2945 " distance=2.04 Simple disulfide: pdb=" SG CYS B2950 " - pdb=" SG CYS B2967 " distance=2.03 Simple disulfide: pdb=" SG CYS B2957 " - pdb=" SG CYS B2980 " distance=2.03 Simple disulfide: pdb=" SG CYS B2974 " - pdb=" SG CYS B2990 " distance=2.03 Simple disulfide: pdb=" SG CYS B2995 " - pdb=" SG CYS B3007 " distance=2.04 Simple disulfide: pdb=" SG CYS B3002 " - pdb=" SG CYS B3020 " distance=2.04 Simple disulfide: pdb=" SG CYS B3014 " - pdb=" SG CYS B3029 " distance=2.04 Simple disulfide: pdb=" SG CYS B3034 " - pdb=" SG CYS B3046 " distance=2.03 Simple disulfide: pdb=" SG CYS B3041 " - pdb=" SG CYS B3059 " distance=2.03 Simple disulfide: pdb=" SG CYS B3053 " - pdb=" SG CYS B3070 " distance=2.04 Simple disulfide: pdb=" SG CYS B3077 " - pdb=" SG CYS B3089 " distance=2.05 Simple disulfide: pdb=" SG CYS B3084 " - pdb=" SG CYS B3102 " distance=2.03 Simple disulfide: pdb=" SG CYS B3096 " - pdb=" SG CYS B3111 " distance=2.03 Simple disulfide: pdb=" SG CYS B3116 " - pdb=" SG CYS B3128 " distance=2.05 Simple disulfide: pdb=" SG CYS B3124 " - pdb=" SG CYS B3137 " distance=2.03 Simple disulfide: pdb=" SG CYS B3139 " - pdb=" SG CYS B3152 " distance=2.03 Simple disulfide: pdb=" SG CYS B3158 " - pdb=" SG CYS B3169 " distance=2.04 Simple disulfide: pdb=" SG CYS B3165 " - pdb=" SG CYS B3178 " distance=2.03 Simple disulfide: pdb=" SG CYS B3180 " - pdb=" SG CYS B3193 " distance=2.04 Simple disulfide: pdb=" SG CYS B3313 " - pdb=" SG CYS B3321 " distance=2.04 Simple disulfide: pdb=" SG CYS B3471 " - pdb=" SG CYS B3482 " distance=2.03 Simple disulfide: pdb=" SG CYS B3478 " - pdb=" SG CYS B3493 " distance=2.05 Simple disulfide: pdb=" SG CYS B3495 " - pdb=" SG CYS B3510 " distance=2.04 Simple disulfide: pdb=" SG CYS B3514 " - pdb=" SG CYS B3527 " distance=2.04 Simple disulfide: pdb=" SG CYS B3521 " - pdb=" SG CYS B3540 " distance=2.03 Simple disulfide: pdb=" SG CYS B3534 " - pdb=" SG CYS B3550 " distance=2.02 Simple disulfide: pdb=" SG CYS B3555 " - pdb=" SG CYS B3567 " distance=2.02 Simple disulfide: pdb=" SG CYS B3562 " - pdb=" SG CYS B3580 " distance=2.05 Simple disulfide: pdb=" SG CYS B3574 " - pdb=" SG CYS B3591 " distance=2.04 Simple disulfide: pdb=" SG CYS B3596 " - pdb=" SG CYS B3608 " distance=2.04 Simple disulfide: pdb=" SG CYS B3603 " - pdb=" SG CYS B3621 " distance=2.04 Simple disulfide: pdb=" SG CYS B3615 " - pdb=" SG CYS B3632 " distance=2.04 Simple disulfide: pdb=" SG CYS B3637 " - pdb=" SG CYS B3649 " distance=2.03 Simple disulfide: pdb=" SG CYS B3644 " - pdb=" SG CYS B3662 " distance=2.04 Simple disulfide: pdb=" SG CYS B3656 " - pdb=" SG CYS B3673 " distance=2.05 Simple disulfide: pdb=" SG CYS B3680 " - pdb=" SG CYS B3694 " distance=2.04 Simple disulfide: pdb=" SG CYS B3688 " - pdb=" SG CYS B3707 " distance=2.03 Simple disulfide: pdb=" SG CYS B3701 " - pdb=" SG CYS B3716 " distance=2.05 Simple disulfide: pdb=" SG CYS B3721 " - pdb=" SG CYS B3734 " distance=2.04 Simple disulfide: pdb=" SG CYS B3729 " - pdb=" SG CYS B3747 " distance=2.04 Simple disulfide: pdb=" SG CYS B3741 " - pdb=" SG CYS B3756 " distance=2.03 Simple disulfide: pdb=" SG CYS B3761 " - pdb=" SG CYS B3773 " distance=2.03 Simple disulfide: pdb=" SG CYS B3768 " - pdb=" SG CYS B3786 " distance=2.04 Simple disulfide: pdb=" SG CYS B3780 " - pdb=" SG CYS B3795 " distance=2.02 Simple disulfide: pdb=" SG CYS B3800 " - pdb=" SG CYS B3812 " distance=2.04 Simple disulfide: pdb=" SG CYS B3807 " - pdb=" SG CYS B3825 " distance=2.04 Simple disulfide: pdb=" SG CYS B3819 " - pdb=" SG CYS B3834 " distance=2.05 Simple disulfide: pdb=" SG CYS B3844 " - pdb=" SG CYS B3856 " distance=2.04 Simple disulfide: pdb=" SG CYS B3851 " - pdb=" SG CYS B3869 " distance=2.03 Simple disulfide: pdb=" SG CYS B3863 " - pdb=" SG CYS B3880 " distance=2.03 Simple disulfide: pdb=" SG CYS B3885 " - pdb=" SG CYS B3898 " distance=2.04 Simple disulfide: pdb=" SG CYS B3893 " - pdb=" SG CYS B3911 " distance=2.03 Simple disulfide: pdb=" SG CYS B3905 " - pdb=" SG CYS B3922 " distance=2.04 Simple disulfide: pdb=" SG CYS B3930 " - pdb=" SG CYS B3942 " distance=2.03 Simple disulfide: pdb=" SG CYS B3937 " - pdb=" SG CYS B3955 " distance=2.02 Simple disulfide: pdb=" SG CYS B3949 " - pdb=" SG CYS B3964 " distance=2.03 Simple disulfide: pdb=" SG CYS B3972 " - pdb=" SG CYS B3981 " distance=2.04 Simple disulfide: pdb=" SG CYS B3977 " - pdb=" SG CYS B3991 " distance=2.03 Simple disulfide: pdb=" SG CYS B3993 " - pdb=" SG CYS B4007 " distance=2.05 Simple disulfide: pdb=" SG CYS B4013 " - pdb=" SG CYS B4023 " distance=2.04 Simple disulfide: pdb=" SG CYS B4019 " - pdb=" SG CYS B4032 " distance=2.04 Simple disulfide: pdb=" SG CYS B4034 " - pdb=" SG CYS B4049 " distance=2.04 Simple disulfide: pdb=" SG CYS B4336 " - pdb=" SG CYS B4344 " distance=2.04 Simple disulfide: pdb=" SG CYS B4340 " - pdb=" SG CYS B4353 " distance=2.04 Simple disulfide: pdb=" SG CYS B4355 " - pdb=" SG CYS B4369 " distance=2.04 Simple disulfide: pdb=" SG CYS B4383 " - pdb=" SG CYS B4391 " distance=2.04 Simple disulfide: pdb=" SG CYS B4385 " - pdb=" SG CYS B4401 " distance=2.04 Simple disulfide: pdb=" SG CYS B4403 " - pdb=" SG CYS B4412 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=22, symmetry=0 Links applied ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 2 3 " - " MAN 2 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " " BMA d 3 " - " MAN d 4 " " BMA g 3 " - " MAN g 4 " " BMA h 3 " - " MAN h 4 " " BMA r 3 " - " MAN r 4 " " BMA t 3 " - " MAN t 4 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 5 " " BMA 2 3 " - " MAN 2 5 " " BMA W 3 " - " MAN W 5 " " BMA Y 3 " - " MAN Y 5 " " BMA d 3 " - " MAN d 5 " " BMA g 3 " - " MAN g 5 " " BMA h 3 " - " MAN h 5 " " BMA r 3 " - " MAN r 5 " " BMA t 3 " - " MAN t 5 " " BMA y 3 " - " MAN y 5 " BETA1-3 " NAG 4 2 " - " BMA 4 3 " " NAG j 2 " - " BMA j 3 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN B3357 " " NAG 1 1 " - " ASN B3566 " " NAG 2 1 " - " ASN B3840 " " NAG 3 1 " - " ASN B4070 " " NAG 4 1 " - " ASN B4329 " " NAG 5 1 " - " ASN B1063 " " NAG A4701 " - " ASN A 340 " " NAG A4702 " - " ASN A 462 " " NAG A4703 " - " ASN A1384 " " NAG A4704 " - " ASN A2134 " " NAG A4705 " - " ASN A2225 " " NAG A4706 " - " ASN A2488 " " NAG A4707 " - " ASN A2782 " " NAG A4708 " - " ASN A2810 " " NAG A4709 " - " ASN A3448 " " NAG A4710 " - " ASN A3682 " " NAG A4711 " - " ASN A3980 " " NAG A4712 " - " ASN A1187 " " NAG B4701 " - " ASN B 340 " " NAG B4702 " - " ASN B 462 " " NAG B4703 " - " ASN B1384 " " NAG B4704 " - " ASN B2134 " " NAG B4705 " - " ASN B2225 " " NAG B4706 " - " ASN B2488 " " NAG B4707 " - " ASN B2782 " " NAG B4708 " - " ASN B2810 " " NAG B4709 " - " ASN B3448 " " NAG B4710 " - " ASN B3682 " " NAG B4711 " - " ASN B3980 " " NAG B4712 " - " ASN B1187 " " NAG E 1 " - " ASN A 657 " " NAG F 1 " - " ASN A 865 " " NAG S 1 " - " ASN A1451 " " NAG T 1 " - " ASN A1497 " " NAG U 1 " - " ASN A1551 " " NAG V 1 " - " ASN A1676 " " NAG W 1 " - " ASN A1733 " " NAG X 1 " - " ASN A1811 " " NAG Y 1 " - " ASN A2178 " " NAG Z 1 " - " ASN A2396 " " NAG a 1 " - " ASN A2548 " " NAG b 1 " - " ASN A3127 " " NAG c 1 " - " ASN A3213 " " NAG d 1 " - " ASN A3259 " " NAG e 1 " - " ASN A3317 " " NAG f 1 " - " ASN A3357 " " NAG g 1 " - " ASN A3566 " " NAG h 1 " - " ASN A3840 " " NAG i 1 " - " ASN A4070 " " NAG j 1 " - " ASN A4329 " " NAG k 1 " - " ASN A1063 " " NAG l 1 " - " ASN B 657 " " NAG m 1 " - " ASN B 865 " " NAG n 1 " - " ASN B1451 " " NAG o 1 " - " ASN B1497 " " NAG p 1 " - " ASN B1551 " " NAG q 1 " - " ASN B1676 " " NAG r 1 " - " ASN B1733 " " NAG s 1 " - " ASN B1811 " " NAG t 1 " - " ASN B2178 " " NAG u 1 " - " ASN B2396 " " NAG v 1 " - " ASN B2548 " " NAG w 1 " - " ASN B3127 " " NAG x 1 " - " ASN B3213 " " NAG y 1 " - " ASN B3259 " " NAG z 1 " - " ASN B3317 " TRANS " UNK G 4 " - " GLU G 3 " " UNK K 4 " - " GLU K 3 " Number of additional bonds: simple=22, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.49 Conformation dependent library (CDL) restraints added in 6.8 seconds 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16048 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 225 sheets defined 8.1% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 17.94 Creating SS restraints... Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.644A pdb=" N ARG A 215 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 660 through 664 removed outlier: 4.123A pdb=" N SER A 664 " --> pdb=" O PRO A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 749 through 751 No H-bonds generated for 'chain 'A' and resid 749 through 751' Processing helix chain 'A' and resid 971 through 975 removed outlier: 3.894A pdb=" N GLN A 975 " --> pdb=" O TYR A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 1041 through 1043 No H-bonds generated for 'chain 'A' and resid 1041 through 1043' Processing helix chain 'A' and resid 1081 through 1085 Processing helix chain 'A' and resid 1095 through 1099 removed outlier: 3.940A pdb=" N GLN A1099 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1138 through 1142 removed outlier: 3.585A pdb=" N LYS A1142 " --> pdb=" O SER A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1205 through 1207 No H-bonds generated for 'chain 'A' and resid 1205 through 1207' Processing helix chain 'A' and resid 1248 through 1250 No H-bonds generated for 'chain 'A' and resid 1248 through 1250' Processing helix chain 'A' and resid 1260 through 1264 removed outlier: 3.598A pdb=" N GLU A1263 " --> pdb=" O GLY A1260 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS A1264 " --> pdb=" O SER A1261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1260 through 1264' Processing helix chain 'A' and resid 1299 through 1303 removed outlier: 4.212A pdb=" N ASP A1302 " --> pdb=" O ASP A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1332 No H-bonds generated for 'chain 'A' and resid 1330 through 1332' Processing helix chain 'A' and resid 1355 through 1361 Processing helix chain 'A' and resid 1694 through 1698 Processing helix chain 'A' and resid 1788 through 1790 No H-bonds generated for 'chain 'A' and resid 1788 through 1790' Processing helix chain 'A' and resid 2021 through 2026 Processing helix chain 'A' and resid 2350 through 2354 Processing helix chain 'A' and resid 2654 through 2663 removed outlier: 3.979A pdb=" N ASP A2657 " --> pdb=" O ASN A2654 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A2658 " --> pdb=" O PRO A2655 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE A2659 " --> pdb=" O CYS A2656 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN A2660 " --> pdb=" O ASP A2657 " (cutoff:3.500A) Processing helix chain 'A' and resid 2717 through 2719 No H-bonds generated for 'chain 'A' and resid 2717 through 2719' Processing helix chain 'A' and resid 2733 through 2738 Processing helix chain 'A' and resid 2758 through 2760 No H-bonds generated for 'chain 'A' and resid 2758 through 2760' Processing helix chain 'A' and resid 2798 through 2800 No H-bonds generated for 'chain 'A' and resid 2798 through 2800' Processing helix chain 'A' and resid 2838 through 2842 Processing helix chain 'A' and resid 2856 through 2861 removed outlier: 3.743A pdb=" N ALA A2861 " --> pdb=" O ILE A2858 " (cutoff:3.500A) Processing helix chain 'A' and resid 2924 through 2926 No H-bonds generated for 'chain 'A' and resid 2924 through 2926' Processing helix chain 'A' and resid 2940 through 2944 Processing helix chain 'A' and resid 2962 through 2966 removed outlier: 3.912A pdb=" N ARG A2966 " --> pdb=" O PRO A2963 " (cutoff:3.500A) Processing helix chain 'A' and resid 2984 through 2989 removed outlier: 4.710A pdb=" N ASN A2989 " --> pdb=" O ASP A2985 " (cutoff:3.500A) Processing helix chain 'A' and resid 3009 through 3013 Processing helix chain 'A' and resid 3091 through 3095 Processing helix chain 'A' and resid 3156 through 3161 Processing helix chain 'A' and resid 3162 through 3165 removed outlier: 4.142A pdb=" N CYS A3165 " --> pdb=" O PRO A3162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3162 through 3165' Processing helix chain 'A' and resid 3332 through 3334 No H-bonds generated for 'chain 'A' and resid 3332 through 3334' Processing helix chain 'A' and resid 3460 through 3464 removed outlier: 3.551A pdb=" N GLN A3464 " --> pdb=" O PRO A3461 " (cutoff:3.500A) Processing helix chain 'A' and resid 3474 through 3478 Processing helix chain 'A' and resid 3531 through 3533 No H-bonds generated for 'chain 'A' and resid 3531 through 3533' Processing helix chain 'A' and resid 3569 through 3573 Processing helix chain 'A' and resid 3583 through 3586 Processing helix chain 'A' and resid 3587 through 3592 removed outlier: 3.554A pdb=" N CYS A3591 " --> pdb=" O ASP A3587 " (cutoff:3.500A) Processing helix chain 'A' and resid 3612 through 3614 No H-bonds generated for 'chain 'A' and resid 3612 through 3614' Processing helix chain 'A' and resid 3628 through 3635 Processing helix chain 'A' and resid 3653 through 3655 No H-bonds generated for 'chain 'A' and resid 3653 through 3655' Processing helix chain 'A' and resid 3669 through 3674 Processing helix chain 'A' and resid 3675 through 3679 removed outlier: 3.753A pdb=" N TYR A3678 " --> pdb=" O THR A3675 " (cutoff:3.500A) Processing helix chain 'A' and resid 3698 through 3700 No H-bonds generated for 'chain 'A' and resid 3698 through 3700' Processing helix chain 'A' and resid 3710 through 3714 Processing helix chain 'A' and resid 3738 through 3740 No H-bonds generated for 'chain 'A' and resid 3738 through 3740' Processing helix chain 'A' and resid 3777 through 3779 No H-bonds generated for 'chain 'A' and resid 3777 through 3779' Processing helix chain 'A' and resid 3816 through 3818 No H-bonds generated for 'chain 'A' and resid 3816 through 3818' Processing helix chain 'A' and resid 3858 through 3862 Processing helix chain 'A' and resid 3872 through 3876 Processing helix chain 'A' and resid 3879 through 3883 Processing helix chain 'A' and resid 3902 through 3904 No H-bonds generated for 'chain 'A' and resid 3902 through 3904' Processing helix chain 'A' and resid 3914 through 3917 Processing helix chain 'A' and resid 3918 through 3923 Processing helix chain 'A' and resid 3946 through 3948 No H-bonds generated for 'chain 'A' and resid 3946 through 3948' Processing helix chain 'A' and resid 3958 through 3962 Processing helix chain 'A' and resid 3971 through 3975 Processing helix chain 'A' and resid 4011 through 4015 Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.631A pdb=" N GLU B 59 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 60 " --> pdb=" O THR B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.557A pdb=" N TYR B 200 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 247 through 251 removed outlier: 4.162A pdb=" N GLY B 251 " --> pdb=" O GLN B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 651 through 655 Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 679 through 684 Processing helix chain 'B' and resid 749 through 751 No H-bonds generated for 'chain 'B' and resid 749 through 751' Processing helix chain 'B' and resid 979 through 983 Processing helix chain 'B' and resid 1039 through 1043 Processing helix chain 'B' and resid 1053 through 1057 Processing helix chain 'B' and resid 1083 through 1085 No H-bonds generated for 'chain 'B' and resid 1083 through 1085' Processing helix chain 'B' and resid 1095 through 1099 removed outlier: 3.535A pdb=" N GLU B1098 " --> pdb=" O GLY B1095 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B1099 " --> pdb=" O SER B1096 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1095 through 1099' Processing helix chain 'B' and resid 1126 through 1128 No H-bonds generated for 'chain 'B' and resid 1126 through 1128' Processing helix chain 'B' and resid 1164 through 1168 removed outlier: 3.855A pdb=" N VAL B1168 " --> pdb=" O PRO B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1207 No H-bonds generated for 'chain 'B' and resid 1205 through 1207' Processing helix chain 'B' and resid 1217 through 1221 Processing helix chain 'B' and resid 1248 through 1250 No H-bonds generated for 'chain 'B' and resid 1248 through 1250' Processing helix chain 'B' and resid 1260 through 1264 removed outlier: 3.524A pdb=" N HIS B1264 " --> pdb=" O SER B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1288 through 1290 No H-bonds generated for 'chain 'B' and resid 1288 through 1290' Processing helix chain 'B' and resid 1300 through 1305 removed outlier: 3.707A pdb=" N ASP B1305 " --> pdb=" O SER B1301 " (cutoff:3.500A) Processing helix chain 'B' and resid 1357 through 1361 Processing helix chain 'B' and resid 1393 through 1397 Processing helix chain 'B' and resid 1694 through 1698 Processing helix chain 'B' and resid 1703 through 1708 Processing helix chain 'B' and resid 1881 through 1883 No H-bonds generated for 'chain 'B' and resid 1881 through 1883' Processing helix chain 'B' and resid 2016 through 2020 removed outlier: 3.673A pdb=" N SER B2020 " --> pdb=" O ALA B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2021 through 2026 Processing helix chain 'B' and resid 2331 through 2335 Processing helix chain 'B' and resid 2349 through 2354 Processing helix chain 'B' and resid 2517 through 2519 No H-bonds generated for 'chain 'B' and resid 2517 through 2519' Processing helix chain 'B' and resid 2657 through 2663 Processing helix chain 'B' and resid 2687 through 2691 Processing helix chain 'B' and resid 2717 through 2719 No H-bonds generated for 'chain 'B' and resid 2717 through 2719' Processing helix chain 'B' and resid 2729 through 2733 removed outlier: 3.601A pdb=" N LEU B2733 " --> pdb=" O SER B2730 " (cutoff:3.500A) Processing helix chain 'B' and resid 2735 through 2740 removed outlier: 4.444A pdb=" N PHE B2739 " --> pdb=" O THR B2735 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS B2740 " --> pdb=" O VAL B2736 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2735 through 2740' Processing helix chain 'B' and resid 2758 through 2760 No H-bonds generated for 'chain 'B' and resid 2758 through 2760' Processing helix chain 'B' and resid 2798 through 2800 No H-bonds generated for 'chain 'B' and resid 2798 through 2800' Processing helix chain 'B' and resid 2838 through 2842 Processing helix chain 'B' and resid 2852 through 2856 Processing helix chain 'B' and resid 2904 through 2908 removed outlier: 4.238A pdb=" N CYS B2908 " --> pdb=" O VAL B2905 " (cutoff:3.500A) Processing helix chain 'B' and resid 2924 through 2926 No H-bonds generated for 'chain 'B' and resid 2924 through 2926' Processing helix chain 'B' and resid 2983 through 2987 Processing helix chain 'B' and resid 3009 through 3013 Processing helix chain 'B' and resid 3048 through 3052 Processing helix chain 'B' and resid 3062 through 3065 Processing helix chain 'B' and resid 3066 through 3071 Processing helix chain 'B' and resid 3093 through 3095 No H-bonds generated for 'chain 'B' and resid 3093 through 3095' Processing helix chain 'B' and resid 3156 through 3161 Processing helix chain 'B' and resid 3162 through 3165 Processing helix chain 'B' and resid 3460 through 3464 Processing helix chain 'B' and resid 3474 through 3478 Processing helix chain 'B' and resid 3531 through 3533 No H-bonds generated for 'chain 'B' and resid 3531 through 3533' Processing helix chain 'B' and resid 3569 through 3573 Processing helix chain 'B' and resid 3583 through 3586 Processing helix chain 'B' and resid 3587 through 3592 Processing helix chain 'B' and resid 3612 through 3614 No H-bonds generated for 'chain 'B' and resid 3612 through 3614' Processing helix chain 'B' and resid 3628 through 3635 Processing helix chain 'B' and resid 3653 through 3655 No H-bonds generated for 'chain 'B' and resid 3653 through 3655' Processing helix chain 'B' and resid 3664 through 3668 removed outlier: 4.317A pdb=" N ASP B3667 " --> pdb=" O ASP B3664 " (cutoff:3.500A) Processing helix chain 'B' and resid 3669 through 3674 Processing helix chain 'B' and resid 3675 through 3679 Processing helix chain 'B' and resid 3698 through 3700 No H-bonds generated for 'chain 'B' and resid 3698 through 3700' Processing helix chain 'B' and resid 3715 through 3719 Processing helix chain 'B' and resid 3738 through 3740 No H-bonds generated for 'chain 'B' and resid 3738 through 3740' Processing helix chain 'B' and resid 3750 through 3754 removed outlier: 3.513A pdb=" N GLU B3754 " --> pdb=" O SER B3751 " (cutoff:3.500A) Processing helix chain 'B' and resid 3777 through 3779 No H-bonds generated for 'chain 'B' and resid 3777 through 3779' Processing helix chain 'B' and resid 3789 through 3793 Processing helix chain 'B' and resid 3816 through 3818 No H-bonds generated for 'chain 'B' and resid 3816 through 3818' Processing helix chain 'B' and resid 3828 through 3833 removed outlier: 4.187A pdb=" N ALA B3833 " --> pdb=" O SER B3829 " (cutoff:3.500A) Processing helix chain 'B' and resid 3860 through 3862 No H-bonds generated for 'chain 'B' and resid 3860 through 3862' Processing helix chain 'B' and resid 3876 through 3881 Processing helix chain 'B' and resid 3902 through 3904 No H-bonds generated for 'chain 'B' and resid 3902 through 3904' Processing helix chain 'B' and resid 3946 through 3948 No H-bonds generated for 'chain 'B' and resid 3946 through 3948' Processing helix chain 'B' and resid 3958 through 3962 Processing helix chain 'B' and resid 3971 through 3975 Processing helix chain 'B' and resid 4011 through 4015 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 73 Processing sheet with id=AA3, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 228 Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 271 Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 323 removed outlier: 3.507A pdb=" N GLN A 319 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 336 through 338 removed outlier: 6.861A pdb=" N THR A 344 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 362 Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AB1, first strand: chain 'A' and resid 413 through 417 removed outlier: 6.915A pdb=" N LEU A 403 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 397 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 428 through 431 removed outlier: 6.784A pdb=" N VAL A 447 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.772A pdb=" N ILE A 490 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 511 through 517 removed outlier: 4.095A pdb=" N GLY A 513 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 522 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 537 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 558 through 564 removed outlier: 4.847A pdb=" N GLY A 560 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 573 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 569 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 579 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 580 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 603 through 608 removed outlier: 4.004A pdb=" N GLY A 605 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 623 " --> pdb=" O TYR A 637 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 672 through 675 Processing sheet with id=AB8, first strand: chain 'A' and resid 694 through 696 Processing sheet with id=AB9, first strand: chain 'A' and resid 732 through 735 removed outlier: 6.544A pdb=" N VAL A 733 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLY A 720 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N HIS A 958 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 742 through 748 removed outlier: 4.696A pdb=" N GLY A 744 " --> pdb=" O SER A 757 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE A 764 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 785 through 791 removed outlier: 4.330A pdb=" N CYS A 787 " --> pdb=" O THR A 800 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 821 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A 809 " --> pdb=" O GLN A 819 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N GLN A 819 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ARG A 811 " --> pdb=" O ARG A 817 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG A 817 " --> pdb=" O ARG A 811 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 827 through 833 removed outlier: 4.522A pdb=" N SER A 829 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 838 " --> pdb=" O HIS A 833 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE A 850 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TRP A 854 " --> pdb=" O HIS A 859 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N HIS A 859 " --> pdb=" O TRP A 854 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 874 through 876 Processing sheet with id=AC5, first strand: chain 'A' and resid 915 through 921 removed outlier: 6.241A pdb=" N THR A 928 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU A 918 " --> pdb=" O PHE A 926 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE A 926 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL A 920 " --> pdb=" O ASN A 924 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASN A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 934 " --> pdb=" O ASP A 929 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 935 " --> pdb=" O ILE A 949 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 986 through 990 Processing sheet with id=AC7, first strand: chain 'A' and resid 1003 through 1005 Processing sheet with id=AC8, first strand: chain 'A' and resid 1029 through 1031 Processing sheet with id=AC9, first strand: chain 'A' and resid 1071 through 1073 removed outlier: 4.621A pdb=" N GLN A1078 " --> pdb=" O CYS A1073 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1114 through 1116 Processing sheet with id=AD2, first strand: chain 'A' and resid 1155 through 1156 Processing sheet with id=AD3, first strand: chain 'A' and resid 1192 through 1194 Processing sheet with id=AD4, first strand: chain 'A' and resid 1235 through 1237 Processing sheet with id=AD5, first strand: chain 'A' and resid 1276 through 1278 Processing sheet with id=AD6, first strand: chain 'A' and resid 1317 through 1318 Processing sheet with id=AD7, first strand: chain 'A' and resid 1365 through 1368 removed outlier: 3.594A pdb=" N GLY A1368 " --> pdb=" O GLY A1371 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 1380 through 1382 Processing sheet with id=AD9, first strand: chain 'A' and resid 1405 through 1408 Processing sheet with id=AE1, first strand: chain 'A' and resid 1420 through 1422 Processing sheet with id=AE2, first strand: chain 'A' and resid 1456 through 1461 removed outlier: 4.185A pdb=" N GLY A1689 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 1469 through 1475 removed outlier: 4.070A pdb=" N ALA A1471 " --> pdb=" O SER A1484 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A1480 " --> pdb=" O ASP A1475 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR A1491 " --> pdb=" O VAL A1504 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 1512 through 1518 removed outlier: 3.788A pdb=" N MET A1514 " --> pdb=" O THR A1527 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A1534 " --> pdb=" O LEU A1547 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 1555 through 1561 removed outlier: 3.900A pdb=" N GLY A1557 " --> pdb=" O SER A1572 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A1568 " --> pdb=" O ASP A1561 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A1580 " --> pdb=" O ILE A1593 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1601 through 1607 removed outlier: 5.092A pdb=" N GLY A1603 " --> pdb=" O MET A1616 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A1623 " --> pdb=" O VAL A1636 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 1646 through 1651 removed outlier: 4.016A pdb=" N ALA A1648 " --> pdb=" O THR A1659 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A1666 " --> pdb=" O VAL A1680 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 1713 through 1716 Processing sheet with id=AE9, first strand: chain 'A' and resid 1732 through 1734 Processing sheet with id=AF1, first strand: chain 'A' and resid 1775 through 1776 removed outlier: 3.561A pdb=" N ILE A1756 " --> pdb=" O ARG A1753 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY A2007 " --> pdb=" O VAL A1752 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 1785 through 1787 removed outlier: 6.876A pdb=" N ILE A1802 " --> pdb=" O PHE A1815 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 1827 through 1830 removed outlier: 6.599A pdb=" N ILE A1846 " --> pdb=" O LEU A1861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 1874 through 1880 removed outlier: 6.450A pdb=" N SER A1889 " --> pdb=" O VAL A1875 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE A1877 " --> pdb=" O TYR A1887 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR A1887 " --> pdb=" O ILE A1877 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL A1879 " --> pdb=" O LYS A1885 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS A1885 " --> pdb=" O VAL A1879 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER A1903 " --> pdb=" O ILE A1913 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILE A1913 " --> pdb=" O SER A1903 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 1922 through 1928 removed outlier: 5.214A pdb=" N VAL A1924 " --> pdb=" O ALA A1937 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A1937 " --> pdb=" O VAL A1924 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A1944 " --> pdb=" O LEU A1957 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 1964 through 1970 removed outlier: 3.832A pdb=" N GLY A1966 " --> pdb=" O SER A1977 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A1984 " --> pdb=" O LEU A1998 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 2033 through 2036 Processing sheet with id=AF8, first strand: chain 'A' and resid 2050 through 2052 Processing sheet with id=AF9, first strand: chain 'A' and resid 2074 through 2077 Processing sheet with id=AG1, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 4.146A pdb=" N HIS A2100 " --> pdb=" O CYS A2113 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A2124 " --> pdb=" O ASP A2114 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A2125 " --> pdb=" O VAL A2138 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 2146 through 2153 removed outlier: 6.689A pdb=" N ILE A2148 " --> pdb=" O ALA A2165 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA A2165 " --> pdb=" O ILE A2148 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY A2150 " --> pdb=" O THR A2163 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR A2170 " --> pdb=" O LYS A2187 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS A2187 " --> pdb=" O THR A2170 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A2172 " --> pdb=" O LEU A2185 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 2193 through 2199 removed outlier: 3.727A pdb=" N HIS A2195 " --> pdb=" O ALA A2208 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A2216 " --> pdb=" O LEU A2229 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 2237 through 2243 removed outlier: 4.048A pdb=" N GLY A2239 " --> pdb=" O VAL A2252 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR A2248 " --> pdb=" O ASP A2243 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 2281 through 2287 removed outlier: 3.913A pdb=" N GLY A2283 " --> pdb=" O VAL A2294 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A2301 " --> pdb=" O ILE A2317 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 2357 through 2359 removed outlier: 3.863A pdb=" N PHE A2357 " --> pdb=" O GLY A2370 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 2375 through 2376 Processing sheet with id=AG8, first strand: chain 'A' and resid 2416 through 2417 removed outlier: 4.965A pdb=" N GLY A2640 " --> pdb=" O SER A2394 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 2421 through 2428 removed outlier: 5.530A pdb=" N ALA A2422 " --> pdb=" O LYS A2439 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LYS A2439 " --> pdb=" O ALA A2422 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA A2424 " --> pdb=" O THR A2437 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG A2444 " --> pdb=" O LEU A2440 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A2447 " --> pdb=" O LEU A2462 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 2471 through 2474 removed outlier: 4.195A pdb=" N GLY A2471 " --> pdb=" O SER A2484 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER A2493 " --> pdb=" O VAL A2503 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL A2503 " --> pdb=" O SER A2493 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 2510 through 2516 removed outlier: 4.359A pdb=" N ALA A2512 " --> pdb=" O THR A2525 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A2532 " --> pdb=" O ASP A2526 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE A2533 " --> pdb=" O ILE A2546 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 2554 through 2559 removed outlier: 3.508A pdb=" N GLY A2556 " --> pdb=" O ALA A2569 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG A2578 " --> pdb=" O VAL A2588 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL A2588 " --> pdb=" O ARG A2578 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 2596 through 2602 removed outlier: 4.882A pdb=" N GLY A2598 " --> pdb=" O THR A2609 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 2666 through 2669 removed outlier: 3.612A pdb=" N ILE A2666 " --> pdb=" O GLN A2677 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 2684 through 2687 Processing sheet with id=AH7, first strand: chain 'A' and resid 2705 through 2707 Processing sheet with id=AH8, first strand: chain 'A' and resid 2746 through 2748 Processing sheet with id=AH9, first strand: chain 'A' and resid 2786 through 2788 removed outlier: 3.685A pdb=" N ILE A2795 " --> pdb=" O PHE A2787 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'A' and resid 2869 through 2871 Processing sheet with id=AI2, first strand: chain 'A' and resid 2912 through 2914 Processing sheet with id=AI3, first strand: chain 'A' and resid 3038 through 3040 Processing sheet with id=AI4, first strand: chain 'A' and resid 3127 through 3130 Processing sheet with id=AI5, first strand: chain 'A' and resid 3143 through 3145 Processing sheet with id=AI6, first strand: chain 'A' and resid 3168 through 3172 Processing sheet with id=AI7, first strand: chain 'A' and resid 3184 through 3186 Processing sheet with id=AI8, first strand: chain 'A' and resid 3221 through 3225 removed outlier: 6.623A pdb=" N ILE A3211 " --> pdb=" O ILE A3224 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A3202 " --> pdb=" O TYR A3459 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A3455 " --> pdb=" O SER A3206 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'A' and resid 3233 through 3237 removed outlier: 4.435A pdb=" N ALA A3233 " --> pdb=" O ILE A3246 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A3253 " --> pdb=" O ILE A3266 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'A' and resid 3274 through 3280 removed outlier: 3.968A pdb=" N SER A3276 " --> pdb=" O LEU A3289 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP A3288 " --> pdb=" O PHE A3297 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A3296 " --> pdb=" O ILE A3309 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'A' and resid 3313 through 3314 removed outlier: 3.996A pdb=" N PHE A3320 " --> pdb=" O VAL A3314 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'A' and resid 3325 through 3331 removed outlier: 5.443A pdb=" N ALA A3340 " --> pdb=" O ARG A3326 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A3328 " --> pdb=" O TYR A3338 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR A3338 " --> pdb=" O ILE A3328 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU A3330 " --> pdb=" O HIS A3336 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N HIS A3336 " --> pdb=" O LEU A3330 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE A3348 " --> pdb=" O ILE A3361 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'A' and resid 3372 through 3375 removed outlier: 6.374A pdb=" N ILE A3391 " --> pdb=" O VAL A3404 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'A' and resid 3412 through 3418 removed outlier: 4.022A pdb=" N ALA A3414 " --> pdb=" O THR A3425 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A3432 " --> pdb=" O LEU A3446 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'A' and resid 3482 through 3484 Processing sheet with id=AJ7, first strand: chain 'A' and resid 3499 through 3503 removed outlier: 3.518A pdb=" N MET A3511 " --> pdb=" O GLN A3500 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'A' and resid 3518 through 3520 Processing sheet with id=AJ9, first strand: chain 'A' and resid 3560 through 3561 Processing sheet with id=AK1, first strand: chain 'A' and resid 3600 through 3602 Processing sheet with id=AK2, first strand: chain 'A' and resid 3641 through 3643 Processing sheet with id=AK3, first strand: chain 'A' and resid 3685 through 3687 Processing sheet with id=AK4, first strand: chain 'A' and resid 3726 through 3728 Processing sheet with id=AK5, first strand: chain 'A' and resid 3765 through 3767 Processing sheet with id=AK6, first strand: chain 'A' and resid 3804 through 3806 Processing sheet with id=AK7, first strand: chain 'A' and resid 3849 through 3850 Processing sheet with id=AK8, first strand: chain 'A' and resid 3890 through 3892 Processing sheet with id=AK9, first strand: chain 'A' and resid 3934 through 3936 Processing sheet with id=AL1, first strand: chain 'A' and resid 3981 through 3983 Processing sheet with id=AL2, first strand: chain 'A' and resid 3997 through 3999 Processing sheet with id=AL3, first strand: chain 'A' and resid 4024 through 4026 Processing sheet with id=AL4, first strand: chain 'A' and resid 4040 through 4043 removed outlier: 3.744A pdb=" N GLY A4046 " --> pdb=" O THR A4043 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'A' and resid 4065 through 4070 Processing sheet with id=AL6, first strand: chain 'A' and resid 4086 through 4092 removed outlier: 4.245A pdb=" N THR A4088 " --> pdb=" O THR A4106 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'A' and resid 4148 through 4152 removed outlier: 3.700A pdb=" N GLY A4148 " --> pdb=" O SER A4161 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A4170 " --> pdb=" O TRP A4180 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TRP A4180 " --> pdb=" O VAL A4170 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'A' and resid 4189 through 4195 removed outlier: 4.452A pdb=" N THR A4204 " --> pdb=" O ALA A4190 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE A4192 " --> pdb=" O PHE A4202 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE A4202 " --> pdb=" O ILE A4192 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL A4194 " --> pdb=" O LEU A4200 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU A4200 " --> pdb=" O VAL A4194 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE A4212 " --> pdb=" O LEU A4225 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'A' and resid 4233 through 4239 removed outlier: 3.594A pdb=" N GLY A4235 " --> pdb=" O SER A4249 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A4256 " --> pdb=" O ILE A4269 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'A' and resid 4276 through 4282 removed outlier: 4.577A pdb=" N SER A4278 " --> pdb=" O VAL A4289 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A4296 " --> pdb=" O VAL A4310 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'A' and resid 4343 through 4347 Processing sheet with id=AM3, first strand: chain 'A' and resid 4390 through 4393 removed outlier: 3.745A pdb=" N ASN A4390 " --> pdb=" O LYS A4402 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'B' and resid 32 through 34 Processing sheet with id=AM5, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AM6, first strand: chain 'B' and resid 188 through 189 Processing sheet with id=AM7, first strand: chain 'B' and resid 226 through 228 Processing sheet with id=AM8, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AM9, first strand: chain 'B' and resid 319 through 323 Processing sheet with id=AN1, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AN2, first strand: chain 'B' and resid 361 through 362 Processing sheet with id=AN3, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AN4, first strand: chain 'B' and resid 413 through 418 removed outlier: 7.168A pdb=" N LEU B 403 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 397 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'B' and resid 428 through 431 removed outlier: 6.882A pdb=" N VAL B 447 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'B' and resid 468 through 474 removed outlier: 4.263A pdb=" N ASN B 470 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 490 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'B' and resid 511 through 517 removed outlier: 6.806A pdb=" N VAL B 537 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE B 541 " --> pdb=" O ASN B 546 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN B 546 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'B' and resid 558 through 564 removed outlier: 4.310A pdb=" N GLY B 560 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR B 579 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 580 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'B' and resid 606 through 609 removed outlier: 6.475A pdb=" N LYS B 625 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL B 636 " --> pdb=" O LYS B 625 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'B' and resid 672 through 675 removed outlier: 3.626A pdb=" N VAL B 672 " --> pdb=" O LYS B 689 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'B' and resid 694 through 696 Processing sheet with id=AO3, first strand: chain 'B' and resid 718 through 721 removed outlier: 6.444A pdb=" N PHE B 709 " --> pdb=" O ALA B 961 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ALA B 961 " --> pdb=" O PHE B 709 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 711 " --> pdb=" O VAL B 959 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL B 959 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N SER B 713 " --> pdb=" O MET B 957 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'B' and resid 742 through 748 removed outlier: 4.196A pdb=" N GLY B 744 " --> pdb=" O SER B 757 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 763 " --> pdb=" O ASP B 758 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 764 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'B' and resid 785 through 791 removed outlier: 4.066A pdb=" N CYS B 787 " --> pdb=" O THR B 800 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 809 " --> pdb=" O GLN B 819 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLN B 819 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ARG B 811 " --> pdb=" O ARG B 817 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG B 817 " --> pdb=" O ARG B 811 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'B' and resid 827 through 833 removed outlier: 4.441A pdb=" N SER B 829 " --> pdb=" O SER B 842 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 850 " --> pdb=" O ILE B 863 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'B' and resid 871 through 876 removed outlier: 3.729A pdb=" N GLY B 873 " --> pdb=" O VAL B 886 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'B' and resid 915 through 921 removed outlier: 3.882A pdb=" N GLY B 917 " --> pdb=" O THR B 928 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 935 " --> pdb=" O ILE B 949 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'B' and resid 986 through 990 Processing sheet with id=AP1, first strand: chain 'B' and resid 1003 through 1005 Processing sheet with id=AP2, first strand: chain 'B' and resid 1030 through 1031 Processing sheet with id=AP3, first strand: chain 'B' and resid 1070 through 1072 Processing sheet with id=AP4, first strand: chain 'B' and resid 1114 through 1116 Processing sheet with id=AP5, first strand: chain 'B' and resid 1155 through 1156 Processing sheet with id=AP6, first strand: chain 'B' and resid 1192 through 1194 Processing sheet with id=AP7, first strand: chain 'B' and resid 1235 through 1237 Processing sheet with id=AP8, first strand: chain 'B' and resid 1276 through 1277 Processing sheet with id=AP9, first strand: chain 'B' and resid 1317 through 1319 Processing sheet with id=AQ1, first strand: chain 'B' and resid 1364 through 1368 removed outlier: 3.737A pdb=" N GLN B1364 " --> pdb=" O LEU B1375 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'B' and resid 1380 through 1382 Processing sheet with id=AQ3, first strand: chain 'B' and resid 1404 through 1408 Processing sheet with id=AQ4, first strand: chain 'B' and resid 1420 through 1422 Processing sheet with id=AQ5, first strand: chain 'B' and resid 1459 through 1461 Processing sheet with id=AQ6, first strand: chain 'B' and resid 1469 through 1475 removed outlier: 4.138A pdb=" N ALA B1471 " --> pdb=" O SER B1484 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR B1491 " --> pdb=" O VAL B1504 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'B' and resid 1512 through 1518 removed outlier: 3.824A pdb=" N MET B1514 " --> pdb=" O THR B1527 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B1534 " --> pdb=" O LEU B1547 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'B' and resid 1555 through 1561 removed outlier: 3.564A pdb=" N GLY B1557 " --> pdb=" O SER B1572 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B1580 " --> pdb=" O ILE B1593 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'B' and resid 1601 through 1607 removed outlier: 4.948A pdb=" N GLY B1603 " --> pdb=" O MET B1616 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B1616 " --> pdb=" O GLY B1603 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE B1623 " --> pdb=" O VAL B1636 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'B' and resid 1646 through 1651 removed outlier: 4.085A pdb=" N ALA B1648 " --> pdb=" O THR B1659 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B1665 " --> pdb=" O ASP B1660 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN B1668 " --> pdb=" O VAL B1679 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL B1679 " --> pdb=" O GLN B1668 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'B' and resid 1713 through 1716 Processing sheet with id=AR3, first strand: chain 'B' and resid 1732 through 1734 Processing sheet with id=AR4, first strand: chain 'B' and resid 1757 through 1761 removed outlier: 4.117A pdb=" N GLY B2007 " --> pdb=" O VAL B1752 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'B' and resid 1785 through 1787 removed outlier: 6.916A pdb=" N ILE B1802 " --> pdb=" O PHE B1815 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'B' and resid 1827 through 1830 removed outlier: 6.637A pdb=" N ILE B1846 " --> pdb=" O LEU B1861 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'B' and resid 1874 through 1880 removed outlier: 3.824A pdb=" N GLY B1876 " --> pdb=" O SER B1889 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B1901 " --> pdb=" O LEU B1914 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'B' and resid 1922 through 1928 removed outlier: 5.292A pdb=" N VAL B1924 " --> pdb=" O ALA B1937 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B1937 " --> pdb=" O VAL B1924 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B1944 " --> pdb=" O LEU B1957 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'B' and resid 1964 through 1970 removed outlier: 3.619A pdb=" N GLY B1966 " --> pdb=" O SER B1977 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B1999 " --> pdb=" O ILE B1984 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG B1986 " --> pdb=" O VAL B1997 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL B1997 " --> pdb=" O ARG B1986 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'B' and resid 2033 through 2036 Processing sheet with id=AS2, first strand: chain 'B' and resid 2050 through 2052 Processing sheet with id=AS3, first strand: chain 'B' and resid 2074 through 2078 Processing sheet with id=AS4, first strand: chain 'B' and resid 2098 through 2104 removed outlier: 4.244A pdb=" N HIS B2100 " --> pdb=" O CYS B2113 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B2125 " --> pdb=" O VAL B2138 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'B' and resid 2148 through 2154 removed outlier: 6.082A pdb=" N ILE B2148 " --> pdb=" O ALA B2165 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B2165 " --> pdb=" O ILE B2148 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B2150 " --> pdb=" O THR B2163 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR B2170 " --> pdb=" O LYS B2187 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS B2187 " --> pdb=" O THR B2170 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B2172 " --> pdb=" O LEU B2185 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'B' and resid 2193 through 2199 removed outlier: 3.747A pdb=" N HIS B2195 " --> pdb=" O ALA B2208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE B2216 " --> pdb=" O LEU B2229 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'B' and resid 2237 through 2243 removed outlier: 4.285A pdb=" N GLY B2239 " --> pdb=" O VAL B2252 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR B2248 " --> pdb=" O ASP B2243 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG B2261 " --> pdb=" O VAL B2271 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL B2271 " --> pdb=" O ARG B2261 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'B' and resid 2281 through 2287 removed outlier: 4.008A pdb=" N GLY B2283 " --> pdb=" O VAL B2294 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B2300 " --> pdb=" O ASP B2295 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B2301 " --> pdb=" O ILE B2317 " (cutoff:3.500A) Processing sheet with id=AS9, first strand: chain 'B' and resid 2357 through 2359 Processing sheet with id=AT1, first strand: chain 'B' and resid 2375 through 2376 Processing sheet with id=AT2, first strand: chain 'B' and resid 2416 through 2417 removed outlier: 4.033A pdb=" N GLY B2640 " --> pdb=" O SER B2394 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'B' and resid 2421 through 2428 removed outlier: 5.906A pdb=" N ALA B2422 " --> pdb=" O LYS B2439 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS B2439 " --> pdb=" O ALA B2422 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA B2424 " --> pdb=" O THR B2437 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY B2445 " --> pdb=" O SER B2464 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N SER B2464 " --> pdb=" O GLY B2445 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B2447 " --> pdb=" O LEU B2462 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'B' and resid 2469 through 2474 removed outlier: 4.179A pdb=" N GLY B2471 " --> pdb=" O SER B2484 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE B2491 " --> pdb=" O ALA B2502 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA B2502 " --> pdb=" O ILE B2491 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N SER B2493 " --> pdb=" O ASN B2500 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN B2500 " --> pdb=" O SER B2493 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'B' and resid 2510 through 2516 removed outlier: 6.266A pdb=" N TRP B2527 " --> pdb=" O PRO B2510 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA B2512 " --> pdb=" O THR B2525 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B2533 " --> pdb=" O ILE B2546 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'B' and resid 2554 through 2560 removed outlier: 6.743A pdb=" N ILE B2576 " --> pdb=" O VAL B2589 " (cutoff:3.500A) Processing sheet with id=AT7, first strand: chain 'B' and resid 2596 through 2602 removed outlier: 3.942A pdb=" N GLY B2598 " --> pdb=" O THR B2609 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B2615 " --> pdb=" O ASP B2610 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'B' and resid 2666 through 2668 removed outlier: 3.609A pdb=" N ILE B2666 " --> pdb=" O GLN B2677 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'B' and resid 2684 through 2686 Processing sheet with id=AU1, first strand: chain 'B' and resid 2705 through 2708 removed outlier: 5.267A pdb=" N CYS B2708 " --> pdb=" O HIS B2712 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N HIS B2712 " --> pdb=" O CYS B2708 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'B' and resid 2746 through 2748 Processing sheet with id=AU3, first strand: chain 'B' and resid 2786 through 2788 Processing sheet with id=AU4, first strand: chain 'B' and resid 2828 through 2829 Processing sheet with id=AU5, first strand: chain 'B' and resid 2869 through 2872 Processing sheet with id=AU6, first strand: chain 'B' and resid 2912 through 2914 Processing sheet with id=AU7, first strand: chain 'B' and resid 2955 through 2956 Processing sheet with id=AU8, first strand: chain 'B' and resid 3000 through 3001 Processing sheet with id=AU9, first strand: chain 'B' and resid 3039 through 3040 Processing sheet with id=AV1, first strand: chain 'B' and resid 3081 through 3082 Processing sheet with id=AV2, first strand: chain 'B' and resid 3127 through 3130 Processing sheet with id=AV3, first strand: chain 'B' and resid 3143 through 3145 Processing sheet with id=AV4, first strand: chain 'B' and resid 3169 through 3172 Processing sheet with id=AV5, first strand: chain 'B' and resid 3184 through 3186 Processing sheet with id=AV6, first strand: chain 'B' and resid 3221 through 3226 removed outlier: 6.701A pdb=" N ILE B3211 " --> pdb=" O ILE B3224 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR B3202 " --> pdb=" O TYR B3459 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP B3455 " --> pdb=" O SER B3206 " (cutoff:3.500A) Processing sheet with id=AV7, first strand: chain 'B' and resid 3235 through 3237 removed outlier: 3.569A pdb=" N TRP B3245 " --> pdb=" O GLU B3254 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE B3253 " --> pdb=" O ILE B3266 " (cutoff:3.500A) Processing sheet with id=AV8, first strand: chain 'B' and resid 3274 through 3280 removed outlier: 4.346A pdb=" N SER B3276 " --> pdb=" O LEU B3289 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B3296 " --> pdb=" O ILE B3309 " (cutoff:3.500A) Processing sheet with id=AV9, first strand: chain 'B' and resid 3325 through 3331 removed outlier: 4.678A pdb=" N GLY B3327 " --> pdb=" O ALA B3340 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE B3348 " --> pdb=" O ILE B3361 " (cutoff:3.500A) Processing sheet with id=AW1, first strand: chain 'B' and resid 3371 through 3375 removed outlier: 3.848A pdb=" N ALA B3371 " --> pdb=" O ALA B3384 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B3384 " --> pdb=" O ALA B3371 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B3391 " --> pdb=" O VAL B3404 " (cutoff:3.500A) Processing sheet with id=AW2, first strand: chain 'B' and resid 3412 through 3418 removed outlier: 4.081A pdb=" N ALA B3414 " --> pdb=" O THR B3425 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B3432 " --> pdb=" O LEU B3446 " (cutoff:3.500A) Processing sheet with id=AW3, first strand: chain 'B' and resid 3481 through 3484 Processing sheet with id=AW4, first strand: chain 'B' and resid 3499 through 3503 Processing sheet with id=AW5, first strand: chain 'B' and resid 3518 through 3520 Processing sheet with id=AW6, first strand: chain 'B' and resid 3560 through 3561 Processing sheet with id=AW7, first strand: chain 'B' and resid 3600 through 3602 Processing sheet with id=AW8, first strand: chain 'B' and resid 3641 through 3643 Processing sheet with id=AW9, first strand: chain 'B' and resid 3685 through 3687 Processing sheet with id=AX1, first strand: chain 'B' and resid 3726 through 3728 Processing sheet with id=AX2, first strand: chain 'B' and resid 3765 through 3767 Processing sheet with id=AX3, first strand: chain 'B' and resid 3804 through 3806 Processing sheet with id=AX4, first strand: chain 'B' and resid 3848 through 3850 Processing sheet with id=AX5, first strand: chain 'B' and resid 3890 through 3892 Processing sheet with id=AX6, first strand: chain 'B' and resid 3934 through 3936 Processing sheet with id=AX7, first strand: chain 'B' and resid 3980 through 3983 removed outlier: 3.789A pdb=" N ASN B3980 " --> pdb=" O SER B3992 " (cutoff:3.500A) Processing sheet with id=AX8, first strand: chain 'B' and resid 3997 through 3999 Processing sheet with id=AX9, first strand: chain 'B' and resid 4024 through 4026 Processing sheet with id=AY1, first strand: chain 'B' and resid 4040 through 4043 removed outlier: 3.728A pdb=" N GLY B4046 " --> pdb=" O THR B4043 " (cutoff:3.500A) Processing sheet with id=AY2, first strand: chain 'B' and resid 4076 through 4077 removed outlier: 3.743A pdb=" N SER B4077 " --> pdb=" O LYS B4068 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS B4068 " --> pdb=" O SER B4077 " (cutoff:3.500A) Processing sheet with id=AY3, first strand: chain 'B' and resid 4086 through 4092 removed outlier: 4.168A pdb=" N THR B4088 " --> pdb=" O THR B4106 " (cutoff:3.500A) Processing sheet with id=AY4, first strand: chain 'B' and resid 4148 through 4152 removed outlier: 3.713A pdb=" N GLY B4148 " --> pdb=" O SER B4161 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL B4170 " --> pdb=" O TRP B4180 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP B4180 " --> pdb=" O VAL B4170 " (cutoff:3.500A) Processing sheet with id=AY5, first strand: chain 'B' and resid 4189 through 4195 removed outlier: 4.441A pdb=" N THR B4204 " --> pdb=" O ALA B4190 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE B4192 " --> pdb=" O PHE B4202 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE B4202 " --> pdb=" O ILE B4192 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL B4194 " --> pdb=" O LEU B4200 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B4200 " --> pdb=" O VAL B4194 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B4212 " --> pdb=" O LEU B4225 " (cutoff:3.500A) Processing sheet with id=AY6, first strand: chain 'B' and resid 4233 through 4239 removed outlier: 3.589A pdb=" N GLY B4235 " --> pdb=" O SER B4249 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B4256 " --> pdb=" O ILE B4269 " (cutoff:3.500A) Processing sheet with id=AY7, first strand: chain 'B' and resid 4276 through 4282 removed outlier: 4.505A pdb=" N SER B4278 " --> pdb=" O VAL B4289 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B4296 " --> pdb=" O VAL B4310 " (cutoff:3.500A) Processing sheet with id=AY8, first strand: chain 'B' and resid 4343 through 4347 Processing sheet with id=AY9, first strand: chain 'B' and resid 4390 through 4393 removed outlier: 3.749A pdb=" N ASN B4390 " --> pdb=" O LYS B4402 " (cutoff:3.500A) 1721 hydrogen bonds defined for protein. 3957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 82.70 Time building geometry restraints manager: 17.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15255 1.33 - 1.46: 18610 1.46 - 1.58: 36811 1.58 - 1.70: 0 1.70 - 1.83: 872 Bond restraints: 71548 Sorted by residual: bond pdb=" N LYS B3998 " pdb=" CA LYS B3998 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 1.95e+01 bond pdb=" CA SER B 974 " pdb=" CB SER B 974 " ideal model delta sigma weight residual 1.530 1.487 0.043 9.80e-03 1.04e+04 1.94e+01 bond pdb=" N VAL B2837 " pdb=" CA VAL B2837 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.67e+01 bond pdb=" N CYS B 331 " pdb=" CA CYS B 331 " ideal model delta sigma weight residual 1.453 1.491 -0.038 9.20e-03 1.18e+04 1.67e+01 bond pdb=" N PHE B3838 " pdb=" CA PHE B3838 " ideal model delta sigma weight residual 1.453 1.485 -0.032 8.30e-03 1.45e+04 1.48e+01 ... (remaining 71543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 87163 2.05 - 4.10: 9200 4.10 - 6.15: 746 6.15 - 8.21: 57 8.21 - 10.26: 8 Bond angle restraints: 97174 Sorted by residual: angle pdb=" CA ASP A3916 " pdb=" CB ASP A3916 " pdb=" CG ASP A3916 " ideal model delta sigma weight residual 112.60 121.23 -8.63 1.00e+00 1.00e+00 7.46e+01 angle pdb=" CA ASP A3300 " pdb=" CB ASP A3300 " pdb=" CG ASP A3300 " ideal model delta sigma weight residual 112.60 120.56 -7.96 1.00e+00 1.00e+00 6.33e+01 angle pdb=" CA ASP A3315 " pdb=" CB ASP A3315 " pdb=" CG ASP A3315 " ideal model delta sigma weight residual 112.60 120.43 -7.83 1.00e+00 1.00e+00 6.13e+01 angle pdb=" CA PHE A 986 " pdb=" CB PHE A 986 " pdb=" CG PHE A 986 " ideal model delta sigma weight residual 113.80 121.12 -7.32 1.00e+00 1.00e+00 5.35e+01 angle pdb=" CA ASP B 923 " pdb=" CB ASP B 923 " pdb=" CG ASP B 923 " ideal model delta sigma weight residual 112.60 119.27 -6.67 1.00e+00 1.00e+00 4.45e+01 ... (remaining 97169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.51: 42222 22.51 - 45.03: 2625 45.03 - 67.54: 461 67.54 - 90.06: 223 90.06 - 112.57: 80 Dihedral angle restraints: 45611 sinusoidal: 20611 harmonic: 25000 Sorted by residual: dihedral pdb=" CB CYS B 973 " pdb=" SG CYS B 973 " pdb=" SG CYS B 987 " pdb=" CB CYS B 987 " ideal model delta sinusoidal sigma weight residual -86.00 -175.83 89.83 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS B2371 " pdb=" SG CYS B2371 " pdb=" SG CYS B2383 " pdb=" CB CYS B2383 " ideal model delta sinusoidal sigma weight residual 93.00 -177.62 -89.38 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS B3534 " pdb=" SG CYS B3534 " pdb=" SG CYS B3550 " pdb=" CB CYS B3550 " ideal model delta sinusoidal sigma weight residual 93.00 -179.77 -87.23 1 1.00e+01 1.00e-02 9.14e+01 ... (remaining 45608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 8576 0.102 - 0.205: 2041 0.205 - 0.307: 122 0.307 - 0.410: 19 0.410 - 0.512: 6 Chirality restraints: 10764 Sorted by residual: chirality pdb=" C1 BMA j 3 " pdb=" O3 NAG j 2 " pdb=" C2 BMA j 3 " pdb=" O5 BMA j 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.32e+01 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.32e+01 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.32e+01 ... (remaining 10761 not shown) Planarity restraints: 12838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B4706 " 0.318 2.00e-02 2.50e+03 2.77e-01 9.57e+02 pdb=" C7 NAG B4706 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG B4706 " 0.142 2.00e-02 2.50e+03 pdb=" N2 NAG B4706 " -0.494 2.00e-02 2.50e+03 pdb=" O7 NAG B4706 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A4710 " -0.293 2.00e-02 2.50e+03 2.48e-01 7.66e+02 pdb=" C7 NAG A4710 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A4710 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG A4710 " 0.424 2.00e-02 2.50e+03 pdb=" O7 NAG A4710 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.293 2.00e-02 2.50e+03 2.48e-01 7.66e+02 pdb=" C7 NAG F 2 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.424 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.029 2.00e-02 2.50e+03 ... (remaining 12835 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 514 2.49 - 3.09: 48949 3.09 - 3.69: 104530 3.69 - 4.30: 155149 4.30 - 4.90: 256698 Nonbonded interactions: 565840 Sorted by model distance: nonbonded pdb=" OE2 GLU A3668 " pdb="CA CA A4759 " model vdw 1.881 2.510 nonbonded pdb=" OD1 ASP B 92 " pdb="CA CA B4725 " model vdw 1.907 2.510 nonbonded pdb=" OD1 ASP B 252 " pdb="CA CA B4727 " model vdw 1.961 2.510 nonbonded pdb=" OE2 GLU B 99 " pdb="CA CA B4725 " model vdw 1.987 2.510 nonbonded pdb=" OD2 ASP B3626 " pdb="CA CA B4758 " model vdw 2.007 2.510 ... (remaining 565835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '3' selection = chain '5' selection = chain 'F' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'z' } ncs_group { reference = chain '1' selection = chain '2' selection = chain 'W' selection = chain 'Y' selection = chain 'd' selection = chain 'g' selection = chain 'h' selection = chain 'r' selection = chain 't' selection = chain 'y' } ncs_group { reference = chain '4' selection = chain 'E' selection = chain 'T' selection = chain 'b' selection = chain 'c' selection = chain 'j' selection = chain 'l' selection = chain 'o' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' selection = chain 'O' selection = chain 'R' } ncs_group { reference = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'N' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.930 Check model and map are aligned: 0.380 Set scattering table: 0.470 Process input model: 185.850 Find NCS groups from input model: 3.470 Set up NCS constraints: 0.710 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.063 71548 Z= 0.718 Angle : 1.282 10.258 97174 Z= 0.837 Chirality : 0.082 0.512 10764 Planarity : 0.012 0.277 12770 Dihedral : 16.157 112.569 28642 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.60 % Favored : 92.34 % Rotamer: Outliers : 2.29 % Allowed : 10.85 % Favored : 86.86 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.09), residues: 8608 helix: -3.49 (0.27), residues: 157 sheet: -0.62 (0.11), residues: 1980 loop : -0.83 (0.08), residues: 6471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.007 TRP B4288 HIS 0.016 0.003 HIS A 908 PHE 0.077 0.006 PHE A 986 TYR 0.110 0.007 TYR B 650 ARG 0.020 0.002 ARG A2096 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 855 time to evaluate : 5.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.6563 (OUTLIER) cc_final: 0.6170 (mt0) REVERT: A 308 MET cc_start: 0.5936 (mmt) cc_final: 0.5688 (tpp) REVERT: A 506 GLU cc_start: 0.8644 (tt0) cc_final: 0.8384 (tm-30) REVERT: A 508 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6715 (mt) REVERT: A 547 ARG cc_start: 0.6397 (mtp180) cc_final: 0.5828 (mtp180) REVERT: A 582 THR cc_start: 0.4780 (OUTLIER) cc_final: 0.4161 (t) REVERT: A 728 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6075 (mm-40) REVERT: A 786 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7144 (mt-10) REVERT: A 841 LEU cc_start: 0.8935 (pt) cc_final: 0.8722 (tt) REVERT: A 842 SER cc_start: 0.8530 (t) cc_final: 0.8304 (p) REVERT: A 901 LEU cc_start: 0.7204 (mt) cc_final: 0.6861 (pp) REVERT: A 919 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8275 (m) REVERT: A 957 MET cc_start: 0.7718 (mmt) cc_final: 0.7123 (mmp) REVERT: A 1119 ASN cc_start: 0.4733 (t0) cc_final: 0.4385 (p0) REVERT: A 1215 ARG cc_start: 0.6414 (tpp-160) cc_final: 0.5948 (mmp-170) REVERT: A 1233 LEU cc_start: 0.8669 (mt) cc_final: 0.8369 (tt) REVERT: A 1319 GLN cc_start: 0.2898 (OUTLIER) cc_final: 0.2659 (tp-100) REVERT: A 1351 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6366 (mp10) REVERT: A 1602 CYS cc_start: 0.8202 (t) cc_final: 0.7557 (p) REVERT: A 1654 ASP cc_start: 0.7022 (m-30) cc_final: 0.6144 (t0) REVERT: A 1737 ASP cc_start: 0.9013 (m-30) cc_final: 0.8679 (p0) REVERT: A 1739 VAL cc_start: 0.8160 (m) cc_final: 0.7866 (p) REVERT: A 1755 ASN cc_start: 0.7799 (t0) cc_final: 0.7310 (t0) REVERT: A 1931 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7792 (tp30) REVERT: A 2188 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8011 (p) REVERT: A 2242 MET cc_start: 0.8429 (tpt) cc_final: 0.8092 (tpt) REVERT: A 2274 TYR cc_start: 0.8484 (t80) cc_final: 0.8208 (t80) REVERT: A 2702 ASN cc_start: 0.8148 (t0) cc_final: 0.7941 (t0) REVERT: A 2885 CYS cc_start: 0.2318 (m) cc_final: 0.2068 (p) REVERT: A 3205 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6419 (t80) REVERT: A 3207 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7435 (t160) REVERT: A 3249 GLU cc_start: 0.8547 (tt0) cc_final: 0.8125 (tm-30) REVERT: A 3262 ASN cc_start: 0.8094 (t0) cc_final: 0.7619 (t0) REVERT: A 3281 TRP cc_start: 0.7826 (p90) cc_final: 0.7345 (p90) REVERT: A 3282 VAL cc_start: 0.7481 (t) cc_final: 0.7181 (t) REVERT: A 3287 TYR cc_start: 0.6302 (m-80) cc_final: 0.6086 (m-10) REVERT: A 3318 ASN cc_start: 0.6934 (OUTLIER) cc_final: 0.6633 (m-40) REVERT: A 3338 TYR cc_start: 0.5636 (m-80) cc_final: 0.5020 (m-80) REVERT: A 3372 ILE cc_start: 0.8269 (tt) cc_final: 0.8007 (pt) REVERT: A 3416 THR cc_start: 0.7265 (OUTLIER) cc_final: 0.6816 (p) REVERT: A 3456 ILE cc_start: 0.8555 (tt) cc_final: 0.8177 (tp) REVERT: A 3531 TRP cc_start: 0.7318 (p90) cc_final: 0.6804 (p90) REVERT: A 3760 GLU cc_start: 0.7153 (pm20) cc_final: 0.6735 (mm-30) REVERT: A 4078 GLU cc_start: 0.5846 (tm-30) cc_final: 0.5349 (tp30) REVERT: A 4114 PHE cc_start: 0.5803 (m-80) cc_final: 0.5131 (m-10) REVERT: A 4176 ARG cc_start: 0.5070 (mtm110) cc_final: 0.4493 (mtm180) REVERT: A 4208 LYS cc_start: 0.7130 (ttpt) cc_final: 0.6918 (tptp) REVERT: A 4217 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6117 (mmt) REVERT: A 4261 TYR cc_start: 0.6867 (p90) cc_final: 0.6528 (p90) REVERT: A 4271 ASN cc_start: 0.7058 (p0) cc_final: 0.6769 (t0) REVERT: A 4274 MET cc_start: 0.6140 (mtm) cc_final: 0.5890 (ptp) REVERT: A 4295 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7211 (mt-10) REVERT: A 4311 LEU cc_start: 0.7866 (pp) cc_final: 0.7607 (pt) REVERT: A 4322 ILE cc_start: 0.5393 (mp) cc_final: 0.4709 (tp) REVERT: A 4370 ASP cc_start: 0.6154 (p0) cc_final: 0.5525 (m-30) REVERT: B 324 PRO cc_start: -0.0693 (Cg_exo) cc_final: -0.0965 (Cg_endo) REVERT: B 352 GLN cc_start: 0.7016 (tm-30) cc_final: 0.6638 (mp10) REVERT: B 379 GLU cc_start: 0.6728 (tm-30) cc_final: 0.6352 (mt-10) REVERT: B 500 ARG cc_start: 0.5306 (OUTLIER) cc_final: 0.4642 (tmm160) REVERT: B 527 ASP cc_start: 0.7467 (p0) cc_final: 0.7023 (p0) REVERT: B 701 HIS cc_start: 0.6614 (m170) cc_final: 0.6404 (m170) REVERT: B 762 ASP cc_start: 0.7366 (m-30) cc_final: 0.6464 (t0) REVERT: B 957 MET cc_start: 0.7800 (mmm) cc_final: 0.7519 (mmm) REVERT: B 968 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7592 (p) REVERT: B 1003 MET cc_start: 0.6431 (mtm) cc_final: 0.5951 (ttm) REVERT: B 1013 GLU cc_start: 0.7595 (tt0) cc_final: 0.7261 (tm-30) REVERT: B 1088 ARG cc_start: 0.7362 (mmt90) cc_final: 0.6930 (tmm160) REVERT: B 1215 ARG cc_start: 0.7628 (tpm170) cc_final: 0.7404 (mtm110) REVERT: B 1396 ASP cc_start: 0.7687 (t0) cc_final: 0.7373 (m-30) REVERT: B 1473 ASP cc_start: 0.7632 (t0) cc_final: 0.7374 (t0) REVERT: B 1535 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8460 (mt-10) REVERT: B 1602 CYS cc_start: 0.8520 (m) cc_final: 0.7723 (p) REVERT: B 1635 GLN cc_start: 0.8943 (mt0) cc_final: 0.8702 (mt0) REVERT: B 1745 ASP cc_start: 0.7892 (m-30) cc_final: 0.7677 (m-30) REVERT: B 1750 MET cc_start: 0.8793 (mtm) cc_final: 0.8518 (mtp) REVERT: B 1770 ASP cc_start: 0.7147 (p0) cc_final: 0.6910 (p0) REVERT: B 1847 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8117 (mt-10) REVERT: B 1912 LYS cc_start: 0.8610 (ttmt) cc_final: 0.8265 (tttp) REVERT: B 1955 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7322 (ppp) REVERT: B 2028 ASN cc_start: 0.8627 (m-40) cc_final: 0.8106 (t0) REVERT: B 2094 GLN cc_start: 0.8701 (tp40) cc_final: 0.8324 (tm-30) REVERT: B 2127 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8506 (ptm160) REVERT: B 2181 TYR cc_start: 0.8435 (m-10) cc_final: 0.8155 (m-10) REVERT: B 2426 ASP cc_start: 0.8699 (t0) cc_final: 0.8300 (p0) REVERT: B 2521 TYR cc_start: 0.8306 (m-80) cc_final: 0.7481 (m-80) REVERT: B 2562 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8506 (tp30) REVERT: B 2706 PHE cc_start: 0.5335 (t80) cc_final: 0.5088 (t80) REVERT: B 2733 LEU cc_start: 0.7699 (tp) cc_final: 0.7411 (mt) REVERT: B 2766 ASP cc_start: 0.5967 (OUTLIER) cc_final: 0.5647 (p0) REVERT: B 2982 ASP cc_start: 0.3469 (p0) cc_final: 0.2910 (p0) REVERT: B 3042 GLN cc_start: 0.6759 (mt0) cc_final: 0.6340 (tt0) REVERT: B 3067 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6312 (pm20) REVERT: B 3068 HIS cc_start: 0.6066 (t-90) cc_final: 0.5815 (m170) REVERT: B 3150 ARG cc_start: 0.6764 (mmt180) cc_final: 0.6512 (ptt90) REVERT: B 3267 ILE cc_start: 0.8229 (mt) cc_final: 0.8014 (tt) REVERT: B 3271 LEU cc_start: 0.7347 (mm) cc_final: 0.5927 (mp) REVERT: B 3333 GLN cc_start: 0.8945 (tp40) cc_final: 0.8406 (mp10) REVERT: B 3766 PHE cc_start: 0.6850 (t80) cc_final: 0.6478 (t80) REVERT: B 3910 ASP cc_start: 0.4977 (m-30) cc_final: 0.4716 (m-30) REVERT: B 4040 SER cc_start: 0.7520 (t) cc_final: 0.6794 (m) REVERT: B 4062 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7804 (mm-30) REVERT: B 4065 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7264 (ptp90) REVERT: B 4078 GLU cc_start: 0.3800 (OUTLIER) cc_final: 0.2999 (tp30) REVERT: B 4081 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6986 (tp30) REVERT: B 4142 TYR cc_start: 0.8326 (m-10) cc_final: 0.8034 (m-10) REVERT: B 4144 MET cc_start: 0.8348 (mtp) cc_final: 0.7862 (ttt) REVERT: B 4158 ILE cc_start: 0.6574 (tt) cc_final: 0.6360 (pt) REVERT: B 4184 THR cc_start: 0.7658 (p) cc_final: 0.7283 (p) REVERT: B 4187 ASP cc_start: 0.6250 (t0) cc_final: 0.5912 (t0) REVERT: B 4188 GLN cc_start: 0.8199 (mt0) cc_final: 0.7829 (mm110) REVERT: B 4217 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6294 (mtt) REVERT: B 4229 ASN cc_start: 0.6235 (m110) cc_final: 0.5860 (t0) REVERT: B 4232 TRP cc_start: 0.8240 (m-10) cc_final: 0.7847 (m-90) REVERT: B 4274 MET cc_start: 0.6375 (mtm) cc_final: 0.5921 (mpp) REVERT: B 4312 VAL cc_start: 0.7828 (t) cc_final: 0.6668 (t) REVERT: B 4386 MET cc_start: 0.6497 (mtt) cc_final: 0.6101 (ptp) outliers start: 174 outliers final: 45 residues processed: 1004 average time/residue: 0.7170 time to fit residues: 1202.8781 Evaluate side-chains 444 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 377 time to evaluate : 5.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1063 ASN Chi-restraints excluded: chain A residue 1319 GLN Chi-restraints excluded: chain A residue 1351 GLN Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2188 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2692 TYR Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2871 GLN Chi-restraints excluded: chain A residue 3128 CYS Chi-restraints excluded: chain A residue 3205 PHE Chi-restraints excluded: chain A residue 3207 ASN Chi-restraints excluded: chain A residue 3209 TYR Chi-restraints excluded: chain A residue 3315 ASP Chi-restraints excluded: chain A residue 3318 ASN Chi-restraints excluded: chain A residue 3416 THR Chi-restraints excluded: chain A residue 3661 ASP Chi-restraints excluded: chain A residue 3741 CYS Chi-restraints excluded: chain A residue 3898 CYS Chi-restraints excluded: chain A residue 3916 ASP Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 899 ASP Chi-restraints excluded: chain B residue 968 THR Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2766 ASP Chi-restraints excluded: chain B residue 2781 CYS Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3373 THR Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3744 THR Chi-restraints excluded: chain B residue 4062 GLU Chi-restraints excluded: chain B residue 4065 ARG Chi-restraints excluded: chain B residue 4078 GLU Chi-restraints excluded: chain B residue 4217 MET Chi-restraints excluded: chain B residue 4339 VAL Chi-restraints excluded: chain B residue 4353 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 726 optimal weight: 0.0270 chunk 651 optimal weight: 0.8980 chunk 361 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 439 optimal weight: 8.9990 chunk 348 optimal weight: 30.0000 chunk 674 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 chunk 409 optimal weight: 10.0000 chunk 501 optimal weight: 5.9990 chunk 780 optimal weight: 2.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 534 GLN A 612 HIS A 859 HIS A 971 ASN A1203 ASN A1232 HIS A1458 ASN A1670 ASN A1712 HIS A1780 HIS A1864 ASN A1920 GLN A2349 GLN A2834 ASN A2847 ASN A2906 ASN A2943 HIS A2959 ASN A3312 HIS A3318 ASN A3331 HIS A3771 GLN A3782 GLN A3867 ASN A4131 ASN A4195 ASN ** A4234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4390 ASN B 100 GLN ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 ASN B 980 ASN B1104 HIS B1576 HIS ** B1665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1993 ASN B2097 ASN B2107 ASN B2403 HIS B3066 GLN B3126 HIS ** B3207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3733 HIS B3867 ASN B3965 ASN B4131 ASN B4195 ASN ** B4234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4390 ASN N 2 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 71548 Z= 0.238 Angle : 0.702 11.253 97174 Z= 0.368 Chirality : 0.049 0.544 10764 Planarity : 0.005 0.070 12770 Dihedral : 10.480 86.953 13036 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.98 % Favored : 94.01 % Rotamer: Outliers : 2.38 % Allowed : 12.48 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.09), residues: 8608 helix: -3.13 (0.31), residues: 167 sheet: -0.71 (0.10), residues: 2306 loop : -0.56 (0.08), residues: 6135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 557 HIS 0.021 0.001 HIS B3071 PHE 0.051 0.002 PHE A4033 TYR 0.022 0.002 TYR A2859 ARG 0.011 0.001 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 411 time to evaluate : 6.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6464 (mt0) REVERT: A 308 MET cc_start: 0.5939 (mmt) cc_final: 0.5519 (tmm) REVERT: A 506 GLU cc_start: 0.8640 (tt0) cc_final: 0.8388 (tm-30) REVERT: A 508 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7097 (mt) REVERT: A 728 GLN cc_start: 0.6444 (OUTLIER) cc_final: 0.6070 (mm-40) REVERT: A 825 ASN cc_start: 0.7333 (m-40) cc_final: 0.7075 (m-40) REVERT: A 861 MET cc_start: 0.7229 (ptt) cc_final: 0.7020 (ptt) REVERT: A 912 MET cc_start: 0.7736 (ttm) cc_final: 0.7532 (tmm) REVERT: A 957 MET cc_start: 0.7626 (mmt) cc_final: 0.7346 (mmp) REVERT: A 1215 ARG cc_start: 0.6307 (tpp-160) cc_final: 0.5817 (mmp-170) REVERT: A 1230 MET cc_start: 0.6222 (mtm) cc_final: 0.5525 (mmm) REVERT: A 1233 LEU cc_start: 0.8334 (mt) cc_final: 0.8017 (tt) REVERT: A 1602 CYS cc_start: 0.7625 (t) cc_final: 0.6950 (p) REVERT: A 1654 ASP cc_start: 0.6850 (m-30) cc_final: 0.6138 (t0) REVERT: A 1737 ASP cc_start: 0.8932 (m-30) cc_final: 0.8603 (p0) REVERT: A 1739 VAL cc_start: 0.8201 (m) cc_final: 0.7919 (p) REVERT: A 1755 ASN cc_start: 0.7907 (t0) cc_final: 0.7316 (t0) REVERT: A 2249 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8713 (pt) REVERT: A 2274 TYR cc_start: 0.8523 (t80) cc_final: 0.8173 (t80) REVERT: A 2702 ASN cc_start: 0.8370 (t0) cc_final: 0.8129 (t0) REVERT: A 2901 CYS cc_start: 0.3606 (OUTLIER) cc_final: 0.3303 (t) REVERT: A 2959 ASN cc_start: 0.5467 (OUTLIER) cc_final: 0.5253 (t0) REVERT: A 3205 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6194 (t80) REVERT: A 3249 GLU cc_start: 0.8553 (tt0) cc_final: 0.8018 (tm-30) REVERT: A 3262 ASN cc_start: 0.7977 (t0) cc_final: 0.7567 (t0) REVERT: A 3281 TRP cc_start: 0.8046 (p90) cc_final: 0.7495 (p90) REVERT: A 3338 TYR cc_start: 0.5861 (m-80) cc_final: 0.5317 (m-80) REVERT: A 3416 THR cc_start: 0.7289 (OUTLIER) cc_final: 0.6991 (p) REVERT: A 3456 ILE cc_start: 0.8511 (tt) cc_final: 0.8233 (tp) REVERT: A 3760 GLU cc_start: 0.7130 (pm20) cc_final: 0.6630 (mm-30) REVERT: A 4079 TYR cc_start: 0.7290 (t80) cc_final: 0.6764 (t80) REVERT: A 4144 MET cc_start: 0.6907 (mmm) cc_final: 0.6545 (mmm) REVERT: A 4208 LYS cc_start: 0.7063 (ttpt) cc_final: 0.6818 (tptp) REVERT: A 4217 MET cc_start: 0.6877 (mpt) cc_final: 0.5688 (mmm) REVERT: A 4261 TYR cc_start: 0.6878 (p90) cc_final: 0.6436 (p90) REVERT: A 4271 ASN cc_start: 0.7037 (p0) cc_final: 0.6812 (t0) REVERT: A 4322 ILE cc_start: 0.5478 (mp) cc_final: 0.4879 (tp) REVERT: A 4360 ASP cc_start: 0.8323 (t0) cc_final: 0.7649 (m-30) REVERT: A 4370 ASP cc_start: 0.5953 (p0) cc_final: 0.5375 (m-30) REVERT: B 257 GLU cc_start: 0.7534 (mp0) cc_final: 0.7199 (pm20) REVERT: B 500 ARG cc_start: 0.5188 (OUTLIER) cc_final: 0.4766 (tmm160) REVERT: B 527 ASP cc_start: 0.6795 (p0) cc_final: 0.6469 (p0) REVERT: B 621 MET cc_start: 0.5155 (mmm) cc_final: 0.4928 (mmm) REVERT: B 781 ARG cc_start: 0.6122 (mtm-85) cc_final: 0.5575 (mtt-85) REVERT: B 791 ASP cc_start: 0.7711 (t0) cc_final: 0.7449 (t0) REVERT: B 957 MET cc_start: 0.7634 (mmm) cc_final: 0.7139 (mmt) REVERT: B 1003 MET cc_start: 0.6629 (mtm) cc_final: 0.6301 (ttm) REVERT: B 1034 ASN cc_start: 0.6624 (t0) cc_final: 0.6175 (p0) REVERT: B 1088 ARG cc_start: 0.7529 (mmt90) cc_final: 0.7032 (tmm160) REVERT: B 1215 ARG cc_start: 0.7739 (tpm170) cc_final: 0.7435 (mtm110) REVERT: B 1396 ASP cc_start: 0.7494 (t0) cc_final: 0.7153 (m-30) REVERT: B 1473 ASP cc_start: 0.7831 (t0) cc_final: 0.7570 (t0) REVERT: B 1560 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7108 (pp) REVERT: B 1698 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8235 (mm-40) REVERT: B 1750 MET cc_start: 0.8587 (mtm) cc_final: 0.8279 (mtp) REVERT: B 2028 ASN cc_start: 0.8736 (m-40) cc_final: 0.8144 (t0) REVERT: B 2094 GLN cc_start: 0.8730 (tp40) cc_final: 0.8354 (tm-30) REVERT: B 2426 ASP cc_start: 0.8866 (t0) cc_final: 0.8495 (p0) REVERT: B 2562 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8543 (tp30) REVERT: B 2733 LEU cc_start: 0.7594 (tp) cc_final: 0.7203 (mt) REVERT: B 3038 GLN cc_start: 0.5431 (OUTLIER) cc_final: 0.4921 (tp40) REVERT: B 3042 GLN cc_start: 0.6810 (mt0) cc_final: 0.6396 (tt0) REVERT: B 3240 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6940 (tt0) REVERT: B 3333 GLN cc_start: 0.8970 (tp40) cc_final: 0.8405 (mp10) REVERT: B 3513 MET cc_start: 0.6853 (ptm) cc_final: 0.6397 (ptt) REVERT: B 4078 GLU cc_start: 0.3736 (tm-30) cc_final: 0.2997 (tp30) REVERT: B 4188 GLN cc_start: 0.8164 (mt0) cc_final: 0.7799 (mm110) REVERT: B 4229 ASN cc_start: 0.6350 (m110) cc_final: 0.5787 (t0) REVERT: B 4232 TRP cc_start: 0.8315 (m-10) cc_final: 0.7879 (m-90) REVERT: B 4370 ASP cc_start: 0.6819 (p0) cc_final: 0.6479 (p0) outliers start: 181 outliers final: 71 residues processed: 572 average time/residue: 0.7230 time to fit residues: 717.9145 Evaluate side-chains 398 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 315 time to evaluate : 5.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1414 CYS Chi-restraints excluded: chain A residue 1448 ILE Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2175 LEU Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2249 ILE Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2692 TYR Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2901 CYS Chi-restraints excluded: chain A residue 2959 ASN Chi-restraints excluded: chain A residue 3007 CYS Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3128 CYS Chi-restraints excluded: chain A residue 3136 TYR Chi-restraints excluded: chain A residue 3205 PHE Chi-restraints excluded: chain A residue 3209 TYR Chi-restraints excluded: chain A residue 3315 ASP Chi-restraints excluded: chain A residue 3416 THR Chi-restraints excluded: chain A residue 3478 CYS Chi-restraints excluded: chain A residue 3503 GLN Chi-restraints excluded: chain A residue 3593 HIS Chi-restraints excluded: chain A residue 3741 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3916 ASP Chi-restraints excluded: chain A residue 4237 SER Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 1560 LEU Chi-restraints excluded: chain B residue 1698 GLN Chi-restraints excluded: chain B residue 1790 GLU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2167 VAL Chi-restraints excluded: chain B residue 2242 MET Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2781 CYS Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3220 SER Chi-restraints excluded: chain B residue 3256 MET Chi-restraints excluded: chain B residue 3362 ILE Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 4062 GLU Chi-restraints excluded: chain B residue 4365 SER Chi-restraints excluded: chain B residue 4373 SER Chi-restraints excluded: chain B residue 4375 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 434 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 649 optimal weight: 0.7980 chunk 531 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 782 optimal weight: 7.9990 chunk 845 optimal weight: 10.0000 chunk 696 optimal weight: 7.9990 chunk 775 optimal weight: 9.9990 chunk 266 optimal weight: 6.9990 chunk 627 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 HIS A2026 ASN A2084 HIS A2322 ASN A2665 HIS A2959 ASN ** A3207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3714 GLN ** A3733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3782 GLN ** A3789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3854 HIS ** A4234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 602 HIS ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2084 HIS B2677 GLN B3088 HIS B3207 ASN ** B3336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4319 GLN ** B4325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 71548 Z= 0.332 Angle : 0.704 11.275 97174 Z= 0.365 Chirality : 0.050 0.469 10764 Planarity : 0.005 0.056 12770 Dihedral : 9.007 84.555 12975 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.75 % Allowed : 13.68 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.09), residues: 8608 helix: -3.14 (0.31), residues: 161 sheet: -0.85 (0.10), residues: 2294 loop : -0.62 (0.08), residues: 6153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1483 HIS 0.021 0.001 HIS A 435 PHE 0.037 0.002 PHE A2778 TYR 0.028 0.002 TYR A3209 ARG 0.011 0.001 ARG B3049 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 334 time to evaluate : 6.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6774 (mt0) REVERT: A 308 MET cc_start: 0.5391 (mmt) cc_final: 0.4995 (tmm) REVERT: A 666 ASN cc_start: 0.6163 (OUTLIER) cc_final: 0.5892 (t0) REVERT: A 728 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6320 (mp10) REVERT: A 732 MET cc_start: 0.7091 (ttp) cc_final: 0.6835 (ppp) REVERT: A 1215 ARG cc_start: 0.6405 (tpp-160) cc_final: 0.5851 (mmp-170) REVERT: A 1230 MET cc_start: 0.6014 (mtm) cc_final: 0.5273 (mmm) REVERT: A 1233 LEU cc_start: 0.8353 (mt) cc_final: 0.8128 (tt) REVERT: A 1654 ASP cc_start: 0.7083 (m-30) cc_final: 0.6584 (t70) REVERT: A 1737 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8613 (p0) REVERT: A 1739 VAL cc_start: 0.8282 (m) cc_final: 0.7972 (p) REVERT: A 1755 ASN cc_start: 0.8094 (t0) cc_final: 0.7376 (t0) REVERT: A 2079 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7790 (mm) REVERT: A 2088 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8578 (ptm) REVERT: A 2176 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7154 (mmm-85) REVERT: A 2453 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: A 2702 ASN cc_start: 0.8392 (t0) cc_final: 0.8144 (t0) REVERT: A 2990 CYS cc_start: 0.4742 (OUTLIER) cc_final: 0.4521 (t) REVERT: A 3205 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.6481 (t80) REVERT: A 3249 GLU cc_start: 0.8513 (tt0) cc_final: 0.8004 (tm-30) REVERT: A 3262 ASN cc_start: 0.7920 (t0) cc_final: 0.7547 (t0) REVERT: A 3338 TYR cc_start: 0.6180 (m-80) cc_final: 0.5929 (m-80) REVERT: A 3395 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6677 (p0) REVERT: A 3433 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7497 (mp0) REVERT: A 3679 ASN cc_start: 0.6245 (OUTLIER) cc_final: 0.5938 (t0) REVERT: A 3760 GLU cc_start: 0.7168 (pm20) cc_final: 0.6589 (mm-30) REVERT: A 3854 HIS cc_start: 0.7050 (m90) cc_final: 0.6768 (m-70) REVERT: A 3860 PHE cc_start: 0.5147 (p90) cc_final: 0.4733 (p90) REVERT: A 4078 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5325 (tp30) REVERT: A 4108 LEU cc_start: 0.8142 (mm) cc_final: 0.7744 (tp) REVERT: A 4208 LYS cc_start: 0.7224 (ttpt) cc_final: 0.7009 (tptp) REVERT: A 4216 TRP cc_start: 0.5806 (m-10) cc_final: 0.5398 (m-10) REVERT: A 4217 MET cc_start: 0.7051 (mpt) cc_final: 0.5857 (mmm) REVERT: A 4261 TYR cc_start: 0.6635 (p90) cc_final: 0.6077 (p90) REVERT: A 4271 ASN cc_start: 0.7261 (p0) cc_final: 0.7004 (t0) REVERT: A 4274 MET cc_start: 0.6296 (ptp) cc_final: 0.5975 (pmm) REVERT: A 4291 LYS cc_start: 0.7294 (tptt) cc_final: 0.7042 (ptmt) REVERT: A 4370 ASP cc_start: 0.5581 (p0) cc_final: 0.5160 (m-30) REVERT: B 257 GLU cc_start: 0.7419 (mp0) cc_final: 0.7095 (pm20) REVERT: B 699 ASP cc_start: 0.4085 (OUTLIER) cc_final: 0.3843 (p0) REVERT: B 856 ASP cc_start: 0.8184 (m-30) cc_final: 0.7752 (m-30) REVERT: B 957 MET cc_start: 0.7796 (mmm) cc_final: 0.7268 (mmt) REVERT: B 1003 MET cc_start: 0.6951 (mtm) cc_final: 0.6386 (mpp) REVERT: B 1010 MET cc_start: 0.6721 (mtt) cc_final: 0.6400 (mtt) REVERT: B 1034 ASN cc_start: 0.6603 (t0) cc_final: 0.6194 (p0) REVERT: B 1088 ARG cc_start: 0.7539 (mmt90) cc_final: 0.7103 (ttp-110) REVERT: B 1215 ARG cc_start: 0.7784 (tpm170) cc_final: 0.7410 (mtm110) REVERT: B 1298 ARG cc_start: 0.6793 (mmm160) cc_final: 0.6547 (mmm160) REVERT: B 1473 ASP cc_start: 0.7999 (t0) cc_final: 0.7690 (t0) REVERT: B 1698 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8200 (mm-40) REVERT: B 1847 GLU cc_start: 0.8768 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 2028 ASN cc_start: 0.8749 (m-40) cc_final: 0.8211 (t0) REVERT: B 2179 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7769 (p) REVERT: B 2426 ASP cc_start: 0.8602 (t0) cc_final: 0.8319 (p0) REVERT: B 2562 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8539 (tp30) REVERT: B 2733 LEU cc_start: 0.7625 (tp) cc_final: 0.7358 (mt) REVERT: B 2938 ASP cc_start: 0.1126 (OUTLIER) cc_final: 0.0463 (t0) REVERT: B 3038 GLN cc_start: 0.5876 (OUTLIER) cc_final: 0.5662 (tp-100) REVERT: B 3042 GLN cc_start: 0.7064 (mt0) cc_final: 0.6611 (tt0) REVERT: B 3207 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.7335 (m-40) REVERT: B 3308 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7489 (tmm) REVERT: B 3507 ARG cc_start: 0.3528 (OUTLIER) cc_final: 0.3169 (ptm-80) REVERT: B 3786 CYS cc_start: 0.2624 (OUTLIER) cc_final: 0.2317 (m) REVERT: B 3794 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: B 4062 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: B 4066 ILE cc_start: 0.7937 (mm) cc_final: 0.7727 (mm) REVERT: B 4106 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.6859 (t) REVERT: B 4125 PHE cc_start: 0.4840 (p90) cc_final: 0.4615 (p90) REVERT: B 4229 ASN cc_start: 0.6175 (m110) cc_final: 0.5736 (t0) REVERT: B 4232 TRP cc_start: 0.8092 (m-10) cc_final: 0.7544 (m-90) outliers start: 209 outliers final: 100 residues processed: 512 average time/residue: 0.6707 time to fit residues: 597.7189 Evaluate side-chains 404 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 279 time to evaluate : 5.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1616 MET Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1871 VAL Chi-restraints excluded: chain A residue 1931 GLU Chi-restraints excluded: chain A residue 1974 LEU Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2176 ARG Chi-restraints excluded: chain A residue 2179 THR Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2249 ILE Chi-restraints excluded: chain A residue 2254 ASP Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2453 TYR Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2596 SER Chi-restraints excluded: chain A residue 2692 TYR Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2990 CYS Chi-restraints excluded: chain A residue 3079 LEU Chi-restraints excluded: chain A residue 3128 CYS Chi-restraints excluded: chain A residue 3136 TYR Chi-restraints excluded: chain A residue 3205 PHE Chi-restraints excluded: chain A residue 3265 THR Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3314 VAL Chi-restraints excluded: chain A residue 3315 ASP Chi-restraints excluded: chain A residue 3373 THR Chi-restraints excluded: chain A residue 3395 ASP Chi-restraints excluded: chain A residue 3400 HIS Chi-restraints excluded: chain A residue 3497 ASP Chi-restraints excluded: chain A residue 3513 MET Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3593 HIS Chi-restraints excluded: chain A residue 3679 ASN Chi-restraints excluded: chain A residue 3777 ARG Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3916 ASP Chi-restraints excluded: chain A residue 4078 GLU Chi-restraints excluded: chain A residue 4080 LEU Chi-restraints excluded: chain A residue 4103 VAL Chi-restraints excluded: chain A residue 4268 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 699 ASP Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 947 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1569 MET Chi-restraints excluded: chain B residue 1589 MET Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1698 GLN Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2136 THR Chi-restraints excluded: chain B residue 2167 VAL Chi-restraints excluded: chain B residue 2179 THR Chi-restraints excluded: chain B residue 2188 VAL Chi-restraints excluded: chain B residue 2225 ASN Chi-restraints excluded: chain B residue 2242 MET Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2699 THR Chi-restraints excluded: chain B residue 2781 CYS Chi-restraints excluded: chain B residue 2938 ASP Chi-restraints excluded: chain B residue 3038 GLN Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3155 ILE Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3207 ASN Chi-restraints excluded: chain B residue 3220 SER Chi-restraints excluded: chain B residue 3256 MET Chi-restraints excluded: chain B residue 3308 MET Chi-restraints excluded: chain B residue 3362 ILE Chi-restraints excluded: chain B residue 3507 ARG Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3788 ASP Chi-restraints excluded: chain B residue 3790 SER Chi-restraints excluded: chain B residue 3794 ASP Chi-restraints excluded: chain B residue 3970 ARG Chi-restraints excluded: chain B residue 4062 GLU Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4365 SER Chi-restraints excluded: chain B residue 4373 SER Chi-restraints excluded: chain B residue 4375 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 773 optimal weight: 30.0000 chunk 588 optimal weight: 2.9990 chunk 406 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 373 optimal weight: 2.9990 chunk 525 optimal weight: 0.9980 chunk 785 optimal weight: 10.0000 chunk 831 optimal weight: 10.0000 chunk 410 optimal weight: 5.9990 chunk 744 optimal weight: 5.9990 chunk 224 optimal weight: 0.5980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1312 HIS A1457 HIS A1905 ASN A2595 HIS ** A2941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3782 GLN ** A3789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 GLN ** B3336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3772 GLN ** B3804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 71548 Z= 0.247 Angle : 0.632 12.557 97174 Z= 0.327 Chirality : 0.047 0.470 10764 Planarity : 0.004 0.067 12770 Dihedral : 8.064 90.229 12964 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.50 % Allowed : 14.57 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.09), residues: 8608 helix: -3.28 (0.30), residues: 155 sheet: -0.83 (0.11), residues: 2298 loop : -0.61 (0.08), residues: 6155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 844 HIS 0.009 0.001 HIS A1312 PHE 0.018 0.002 PHE A4033 TYR 0.021 0.002 TYR A3209 ARG 0.014 0.000 ARG A4176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 306 time to evaluate : 6.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6680 (mt0) REVERT: A 308 MET cc_start: 0.5455 (mmt) cc_final: 0.5000 (tmm) REVERT: A 666 ASN cc_start: 0.6184 (OUTLIER) cc_final: 0.5902 (t0) REVERT: A 728 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6327 (mm110) REVERT: A 732 MET cc_start: 0.7140 (ttp) cc_final: 0.6838 (ppp) REVERT: A 1215 ARG cc_start: 0.6582 (tpp-160) cc_final: 0.5938 (mmp-170) REVERT: A 1230 MET cc_start: 0.5905 (mtm) cc_final: 0.5232 (mmm) REVERT: A 1233 LEU cc_start: 0.8404 (mt) cc_final: 0.8194 (tt) REVERT: A 1654 ASP cc_start: 0.6993 (m-30) cc_final: 0.6585 (t70) REVERT: A 1737 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8612 (p0) REVERT: A 1739 VAL cc_start: 0.8261 (m) cc_final: 0.7956 (p) REVERT: A 1755 ASN cc_start: 0.8053 (t0) cc_final: 0.7387 (t0) REVERT: A 2079 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7850 (mm) REVERT: A 2088 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8519 (ptm) REVERT: A 2127 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7492 (ptp-170) REVERT: A 2176 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7187 (mmm-85) REVERT: A 2426 ASP cc_start: 0.8696 (t0) cc_final: 0.8429 (t0) REVERT: A 2453 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: A 2702 ASN cc_start: 0.8402 (t0) cc_final: 0.8167 (t0) REVERT: A 2990 CYS cc_start: 0.5559 (OUTLIER) cc_final: 0.5346 (t) REVERT: A 3039 PHE cc_start: 0.3843 (OUTLIER) cc_final: 0.3639 (t80) REVERT: A 3205 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6123 (t80) REVERT: A 3249 GLU cc_start: 0.8505 (tt0) cc_final: 0.7981 (tm-30) REVERT: A 3338 TYR cc_start: 0.6238 (m-80) cc_final: 0.5918 (m-80) REVERT: A 3395 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6516 (p0) REVERT: A 3433 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7464 (mp0) REVERT: A 3760 GLU cc_start: 0.7079 (pm20) cc_final: 0.6481 (mm-30) REVERT: A 3854 HIS cc_start: 0.6688 (m90) cc_final: 0.6332 (m-70) REVERT: A 4216 TRP cc_start: 0.5922 (m-10) cc_final: 0.5551 (m-10) REVERT: A 4217 MET cc_start: 0.6472 (mpt) cc_final: 0.5445 (mmm) REVERT: A 4261 TYR cc_start: 0.6629 (p90) cc_final: 0.6122 (p90) REVERT: A 4274 MET cc_start: 0.5968 (ptp) cc_final: 0.5562 (pmm) REVERT: A 4360 ASP cc_start: 0.8473 (t0) cc_final: 0.7777 (m-30) REVERT: A 4370 ASP cc_start: 0.5567 (p0) cc_final: 0.5194 (m-30) REVERT: B 257 GLU cc_start: 0.7537 (mp0) cc_final: 0.7201 (pm20) REVERT: B 377 ILE cc_start: 0.5382 (OUTLIER) cc_final: 0.5173 (pt) REVERT: B 855 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 856 ASP cc_start: 0.8463 (m-30) cc_final: 0.7968 (m-30) REVERT: B 1003 MET cc_start: 0.6994 (mtm) cc_final: 0.6485 (mpp) REVERT: B 1010 MET cc_start: 0.6616 (mtt) cc_final: 0.6209 (mtt) REVERT: B 1034 ASN cc_start: 0.5729 (t0) cc_final: 0.5368 (p0) REVERT: B 1088 ARG cc_start: 0.7552 (mmt90) cc_final: 0.7125 (ttp-110) REVERT: B 1215 ARG cc_start: 0.7796 (tpm170) cc_final: 0.7387 (mtm110) REVERT: B 1473 ASP cc_start: 0.7913 (t0) cc_final: 0.7676 (t0) REVERT: B 1560 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7393 (pp) REVERT: B 1698 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8183 (mm-40) REVERT: B 1847 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8058 (mt-10) REVERT: B 2179 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7706 (p) REVERT: B 2562 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8504 (tp30) REVERT: B 2733 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7570 (mt) REVERT: B 3042 GLN cc_start: 0.7075 (mt0) cc_final: 0.6744 (tt0) REVERT: B 3308 MET cc_start: 0.7826 (ptm) cc_final: 0.6892 (tmm) REVERT: B 3507 ARG cc_start: 0.3596 (OUTLIER) cc_final: 0.3166 (ptm-80) REVERT: B 3513 MET cc_start: 0.6465 (ptm) cc_final: 0.5994 (ptt) REVERT: B 3786 CYS cc_start: 0.2689 (OUTLIER) cc_final: 0.2369 (m) REVERT: B 4066 ILE cc_start: 0.7936 (mm) cc_final: 0.7684 (mm) REVERT: B 4229 ASN cc_start: 0.7067 (m110) cc_final: 0.6523 (t0) outliers start: 190 outliers final: 106 residues processed: 472 average time/residue: 0.6440 time to fit residues: 534.1577 Evaluate side-chains 397 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 270 time to evaluate : 6.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1384 ASN Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1931 GLU Chi-restraints excluded: chain A residue 1974 LEU Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG Chi-restraints excluded: chain A residue 2176 ARG Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2254 ASP Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2453 TYR Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2692 TYR Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2800 VAL Chi-restraints excluded: chain A residue 2990 CYS Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3039 PHE Chi-restraints excluded: chain A residue 3079 LEU Chi-restraints excluded: chain A residue 3128 CYS Chi-restraints excluded: chain A residue 3136 TYR Chi-restraints excluded: chain A residue 3205 PHE Chi-restraints excluded: chain A residue 3209 TYR Chi-restraints excluded: chain A residue 3232 VAL Chi-restraints excluded: chain A residue 3265 THR Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3314 VAL Chi-restraints excluded: chain A residue 3315 ASP Chi-restraints excluded: chain A residue 3377 THR Chi-restraints excluded: chain A residue 3395 ASP Chi-restraints excluded: chain A residue 3478 CYS Chi-restraints excluded: chain A residue 3497 ASP Chi-restraints excluded: chain A residue 3520 LEU Chi-restraints excluded: chain A residue 3593 HIS Chi-restraints excluded: chain A residue 3597 GLU Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3777 ARG Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3916 ASP Chi-restraints excluded: chain A residue 3970 ARG Chi-restraints excluded: chain A residue 4080 LEU Chi-restraints excluded: chain A residue 4268 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 947 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1296 ASP Chi-restraints excluded: chain B residue 1336 VAL Chi-restraints excluded: chain B residue 1378 LEU Chi-restraints excluded: chain B residue 1560 LEU Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1698 GLN Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2136 THR Chi-restraints excluded: chain B residue 2167 VAL Chi-restraints excluded: chain B residue 2171 LEU Chi-restraints excluded: chain B residue 2179 THR Chi-restraints excluded: chain B residue 2188 VAL Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2713 CYS Chi-restraints excluded: chain B residue 2733 LEU Chi-restraints excluded: chain B residue 2781 CYS Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3155 ILE Chi-restraints excluded: chain B residue 3220 SER Chi-restraints excluded: chain B residue 3256 MET Chi-restraints excluded: chain B residue 3290 ASP Chi-restraints excluded: chain B residue 3362 ILE Chi-restraints excluded: chain B residue 3501 THR Chi-restraints excluded: chain B residue 3507 ARG Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3553 ARG Chi-restraints excluded: chain B residue 3786 CYS Chi-restraints excluded: chain B residue 3788 ASP Chi-restraints excluded: chain B residue 3790 SER Chi-restraints excluded: chain B residue 4268 LEU Chi-restraints excluded: chain B residue 4312 VAL Chi-restraints excluded: chain B residue 4365 SER Chi-restraints excluded: chain B residue 4375 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 692 optimal weight: 8.9990 chunk 471 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 618 optimal weight: 0.6980 chunk 342 optimal weight: 3.9990 chunk 709 optimal weight: 20.0000 chunk 574 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 424 optimal weight: 7.9990 chunk 746 optimal weight: 20.0000 chunk 209 optimal weight: 0.7980 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS A 602 HIS A 638 HIS A1312 HIS A1665 GLN A1803 HIS A2212 GLN A2941 GLN A2948 GLN A3733 HIS A3782 GLN ** A3789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 HIS B1610 ASN ** B3038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3207 ASN ** B3336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 71548 Z= 0.257 Angle : 0.627 10.749 97174 Z= 0.325 Chirality : 0.047 0.438 10764 Planarity : 0.005 0.050 12770 Dihedral : 7.520 73.092 12959 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.07 % Allowed : 14.67 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.09), residues: 8608 helix: -3.19 (0.30), residues: 166 sheet: -0.89 (0.10), residues: 2353 loop : -0.62 (0.08), residues: 6089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 844 HIS 0.009 0.001 HIS A1312 PHE 0.041 0.002 PHE B3989 TYR 0.017 0.002 TYR B1622 ARG 0.007 0.000 ARG A4176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 291 time to evaluate : 6.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6683 (mt0) REVERT: A 259 ASN cc_start: 0.4360 (t0) cc_final: 0.4082 (m110) REVERT: A 308 MET cc_start: 0.5402 (mmt) cc_final: 0.4936 (tmm) REVERT: A 666 ASN cc_start: 0.5851 (OUTLIER) cc_final: 0.5510 (t0) REVERT: A 728 GLN cc_start: 0.6589 (OUTLIER) cc_final: 0.6246 (mm110) REVERT: A 1215 ARG cc_start: 0.6666 (tpp-160) cc_final: 0.6063 (mmp-170) REVERT: A 1654 ASP cc_start: 0.7150 (m-30) cc_final: 0.6764 (t70) REVERT: A 1737 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8606 (p0) REVERT: A 1739 VAL cc_start: 0.8351 (m) cc_final: 0.8027 (p) REVERT: A 1755 ASN cc_start: 0.8078 (t0) cc_final: 0.7401 (t0) REVERT: A 2079 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7843 (mm) REVERT: A 2088 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8534 (ptm) REVERT: A 2127 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.7484 (ptp-170) REVERT: A 2176 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7188 (mmm-85) REVERT: A 2426 ASP cc_start: 0.8704 (t0) cc_final: 0.8435 (t0) REVERT: A 2453 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7317 (m-80) REVERT: A 2702 ASN cc_start: 0.8258 (t0) cc_final: 0.8021 (t0) REVERT: A 2990 CYS cc_start: 0.5339 (OUTLIER) cc_final: 0.5123 (t) REVERT: A 3205 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.5812 (t80) REVERT: A 3235 ASP cc_start: 0.8127 (t0) cc_final: 0.7535 (t0) REVERT: A 3240 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6800 (mt-10) REVERT: A 3249 GLU cc_start: 0.8324 (tt0) cc_final: 0.7708 (tm-30) REVERT: A 3270 ARG cc_start: 0.7709 (tpp-160) cc_final: 0.7386 (tpp-160) REVERT: A 3395 ASP cc_start: 0.6829 (OUTLIER) cc_final: 0.6520 (p0) REVERT: A 3433 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7425 (mp0) REVERT: A 3760 GLU cc_start: 0.7136 (pm20) cc_final: 0.6487 (mm-30) REVERT: A 3854 HIS cc_start: 0.6678 (m90) cc_final: 0.6310 (m-70) REVERT: A 4144 MET cc_start: 0.7025 (mmm) cc_final: 0.6681 (mmm) REVERT: A 4216 TRP cc_start: 0.5958 (m-10) cc_final: 0.5600 (m-10) REVERT: A 4217 MET cc_start: 0.6287 (OUTLIER) cc_final: 0.4659 (mmt) REVERT: A 4274 MET cc_start: 0.5855 (ptp) cc_final: 0.5526 (pmm) REVERT: A 4370 ASP cc_start: 0.5548 (p0) cc_final: 0.5165 (m-30) REVERT: B 257 GLU cc_start: 0.7546 (mp0) cc_final: 0.7199 (pm20) REVERT: B 426 MET cc_start: 0.6416 (tpt) cc_final: 0.6151 (tpt) REVERT: B 856 ASP cc_start: 0.8451 (m-30) cc_final: 0.8107 (m-30) REVERT: B 905 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7444 (ttt180) REVERT: B 957 MET cc_start: 0.7985 (mmt) cc_final: 0.7481 (mmt) REVERT: B 1003 MET cc_start: 0.7000 (mtm) cc_final: 0.6460 (mpp) REVERT: B 1010 MET cc_start: 0.6608 (mtt) cc_final: 0.6196 (mtt) REVERT: B 1034 ASN cc_start: 0.5787 (t0) cc_final: 0.5396 (p0) REVERT: B 1088 ARG cc_start: 0.7487 (mmt90) cc_final: 0.7099 (ttp-110) REVERT: B 1215 ARG cc_start: 0.7593 (tpm170) cc_final: 0.7180 (mtm110) REVERT: B 1300 MET cc_start: 0.4421 (mmm) cc_final: 0.4116 (tpp) REVERT: B 1560 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7463 (pp) REVERT: B 1698 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8082 (mm-40) REVERT: B 1847 GLU cc_start: 0.8746 (mt-10) cc_final: 0.7934 (mt-10) REVERT: B 2127 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8778 (ptt180) REVERT: B 2179 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7751 (p) REVERT: B 2562 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8552 (tp30) REVERT: B 2733 LEU cc_start: 0.7824 (tp) cc_final: 0.7614 (mt) REVERT: B 3042 GLN cc_start: 0.6974 (mt0) cc_final: 0.6648 (tt0) REVERT: B 3507 ARG cc_start: 0.3179 (OUTLIER) cc_final: 0.2608 (ptm-80) REVERT: B 3794 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6807 (m-30) REVERT: B 4066 ILE cc_start: 0.8020 (mm) cc_final: 0.7735 (mm) REVERT: B 4229 ASN cc_start: 0.7015 (m110) cc_final: 0.6513 (t0) REVERT: B 4261 TYR cc_start: 0.8026 (p90) cc_final: 0.7662 (p90) REVERT: B 4370 ASP cc_start: 0.6511 (p0) cc_final: 0.6209 (m-30) REVERT: B 4379 MET cc_start: 0.4103 (mmp) cc_final: 0.3891 (mmt) outliers start: 233 outliers final: 146 residues processed: 492 average time/residue: 0.7035 time to fit residues: 617.8029 Evaluate side-chains 435 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 269 time to evaluate : 5.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1384 ASN Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1602 CYS Chi-restraints excluded: chain A residue 1616 MET Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1840 THR Chi-restraints excluded: chain A residue 1871 VAL Chi-restraints excluded: chain A residue 1931 GLU Chi-restraints excluded: chain A residue 1974 LEU Chi-restraints excluded: chain A residue 2031 GLN Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG Chi-restraints excluded: chain A residue 2176 ARG Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2254 ASP Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2453 TYR Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2544 VAL Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2596 SER Chi-restraints excluded: chain A residue 2692 TYR Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2800 VAL Chi-restraints excluded: chain A residue 2990 CYS Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3079 LEU Chi-restraints excluded: chain A residue 3128 CYS Chi-restraints excluded: chain A residue 3136 TYR Chi-restraints excluded: chain A residue 3205 PHE Chi-restraints excluded: chain A residue 3232 VAL Chi-restraints excluded: chain A residue 3265 THR Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3314 VAL Chi-restraints excluded: chain A residue 3315 ASP Chi-restraints excluded: chain A residue 3373 THR Chi-restraints excluded: chain A residue 3395 ASP Chi-restraints excluded: chain A residue 3400 HIS Chi-restraints excluded: chain A residue 3497 ASP Chi-restraints excluded: chain A residue 3520 LEU Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3593 HIS Chi-restraints excluded: chain A residue 3621 CYS Chi-restraints excluded: chain A residue 3729 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3777 ARG Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3834 CYS Chi-restraints excluded: chain A residue 3970 ARG Chi-restraints excluded: chain A residue 4080 LEU Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4268 LEU Chi-restraints excluded: chain A residue 4306 ASN Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 699 ASP Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 905 ARG Chi-restraints excluded: chain B residue 947 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1291 CYS Chi-restraints excluded: chain B residue 1296 ASP Chi-restraints excluded: chain B residue 1378 LEU Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1560 LEU Chi-restraints excluded: chain B residue 1589 MET Chi-restraints excluded: chain B residue 1610 ASN Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1681 MET Chi-restraints excluded: chain B residue 1698 GLN Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 1922 LEU Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2136 THR Chi-restraints excluded: chain B residue 2167 VAL Chi-restraints excluded: chain B residue 2171 LEU Chi-restraints excluded: chain B residue 2179 THR Chi-restraints excluded: chain B residue 2188 VAL Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2440 LEU Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2699 THR Chi-restraints excluded: chain B residue 2713 CYS Chi-restraints excluded: chain B residue 2781 CYS Chi-restraints excluded: chain B residue 3035 HIS Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3155 ILE Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3220 SER Chi-restraints excluded: chain B residue 3256 MET Chi-restraints excluded: chain B residue 3290 ASP Chi-restraints excluded: chain B residue 3362 ILE Chi-restraints excluded: chain B residue 3388 LEU Chi-restraints excluded: chain B residue 3422 VAL Chi-restraints excluded: chain B residue 3501 THR Chi-restraints excluded: chain B residue 3507 ARG Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3553 ARG Chi-restraints excluded: chain B residue 3554 PHE Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3788 ASP Chi-restraints excluded: chain B residue 3790 SER Chi-restraints excluded: chain B residue 3794 ASP Chi-restraints excluded: chain B residue 3982 THR Chi-restraints excluded: chain B residue 4136 VAL Chi-restraints excluded: chain B residue 4268 LEU Chi-restraints excluded: chain B residue 4312 VAL Chi-restraints excluded: chain B residue 4365 SER Chi-restraints excluded: chain B residue 4373 SER Chi-restraints excluded: chain B residue 4375 LEU Chi-restraints excluded: chain I residue 3 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 279 optimal weight: 3.9990 chunk 748 optimal weight: 9.9990 chunk 164 optimal weight: 0.7980 chunk 488 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 832 optimal weight: 8.9990 chunk 690 optimal weight: 9.9990 chunk 385 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 275 optimal weight: 4.9990 chunk 436 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 728 GLN A1312 HIS A2710 ASN A3782 GLN ** A3789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B2871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 71548 Z= 0.234 Angle : 0.610 10.563 97174 Z= 0.315 Chirality : 0.047 0.442 10764 Planarity : 0.004 0.060 12770 Dihedral : 7.297 70.927 12956 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.83 % Allowed : 15.19 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.09), residues: 8608 helix: -3.19 (0.29), residues: 161 sheet: -0.84 (0.10), residues: 2329 loop : -0.61 (0.08), residues: 6118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 844 HIS 0.005 0.001 HIS A1505 PHE 0.017 0.001 PHE B1625 TYR 0.021 0.001 TYR A2685 ARG 0.006 0.000 ARG A4176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 286 time to evaluate : 5.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6686 (mt0) REVERT: A 308 MET cc_start: 0.5407 (mmt) cc_final: 0.4936 (tmm) REVERT: A 666 ASN cc_start: 0.6089 (OUTLIER) cc_final: 0.5767 (t0) REVERT: A 1215 ARG cc_start: 0.6665 (tpp-160) cc_final: 0.6055 (mmp-170) REVERT: A 1654 ASP cc_start: 0.7168 (m-30) cc_final: 0.6774 (t70) REVERT: A 1737 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8602 (p0) REVERT: A 1739 VAL cc_start: 0.8337 (m) cc_final: 0.8010 (p) REVERT: A 1755 ASN cc_start: 0.8001 (t0) cc_final: 0.7357 (t0) REVERT: A 2062 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.6280 (m-80) REVERT: A 2079 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7836 (mm) REVERT: A 2088 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8526 (ptm) REVERT: A 2127 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7498 (ptp-170) REVERT: A 2176 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7170 (mmm-85) REVERT: A 2320 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8633 (mptp) REVERT: A 2426 ASP cc_start: 0.8712 (t0) cc_final: 0.8432 (t0) REVERT: A 2453 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: A 2702 ASN cc_start: 0.8182 (t0) cc_final: 0.7946 (t0) REVERT: A 2710 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7341 (p0) REVERT: A 2990 CYS cc_start: 0.5335 (OUTLIER) cc_final: 0.5115 (t) REVERT: A 3029 CYS cc_start: 0.5257 (OUTLIER) cc_final: 0.4856 (p) REVERT: A 3205 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.5693 (t80) REVERT: A 3235 ASP cc_start: 0.8126 (t0) cc_final: 0.7516 (t0) REVERT: A 3240 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6783 (mt-10) REVERT: A 3249 GLU cc_start: 0.8168 (tt0) cc_final: 0.7698 (tm-30) REVERT: A 3270 ARG cc_start: 0.7789 (tpp-160) cc_final: 0.7453 (tpp-160) REVERT: A 3395 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.6446 (p0) REVERT: A 3433 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7406 (mp0) REVERT: A 3760 GLU cc_start: 0.7096 (pm20) cc_final: 0.6504 (mm-30) REVERT: A 4144 MET cc_start: 0.6965 (mmm) cc_final: 0.6682 (mmm) REVERT: A 4216 TRP cc_start: 0.5965 (m-10) cc_final: 0.5632 (m-10) REVERT: A 4217 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.5176 (mmm) REVERT: A 4274 MET cc_start: 0.6224 (ptp) cc_final: 0.5874 (pmm) REVERT: A 4360 ASP cc_start: 0.8367 (t0) cc_final: 0.7712 (m-30) REVERT: A 4370 ASP cc_start: 0.5576 (p0) cc_final: 0.5201 (m-30) REVERT: B 257 GLU cc_start: 0.7544 (mp0) cc_final: 0.7223 (pm20) REVERT: B 426 MET cc_start: 0.6512 (tpt) cc_final: 0.6228 (tpt) REVERT: B 624 MET cc_start: 0.2395 (mtt) cc_final: 0.2185 (mtm) REVERT: B 856 ASP cc_start: 0.8458 (m-30) cc_final: 0.8100 (m-30) REVERT: B 905 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7430 (ttt180) REVERT: B 957 MET cc_start: 0.8010 (mmt) cc_final: 0.7617 (mmp) REVERT: B 1003 MET cc_start: 0.7006 (mtm) cc_final: 0.6473 (mpp) REVERT: B 1010 MET cc_start: 0.6675 (mtt) cc_final: 0.6212 (mtt) REVERT: B 1034 ASN cc_start: 0.5824 (t0) cc_final: 0.5338 (p0) REVERT: B 1088 ARG cc_start: 0.7502 (mmt90) cc_final: 0.7039 (tmm160) REVERT: B 1215 ARG cc_start: 0.7708 (tpm170) cc_final: 0.7294 (mtm110) REVERT: B 1560 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7443 (pp) REVERT: B 1698 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8165 (mm-40) REVERT: B 1847 GLU cc_start: 0.8711 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 1955 MET cc_start: 0.7582 (ptt) cc_final: 0.6422 (ppp) REVERT: B 2127 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8770 (ptt180) REVERT: B 2179 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7755 (p) REVERT: B 2562 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8552 (tp30) REVERT: B 2938 ASP cc_start: 0.0088 (OUTLIER) cc_final: -0.0442 (t0) REVERT: B 3308 MET cc_start: 0.8052 (ptm) cc_final: 0.7566 (tmm) REVERT: B 3507 ARG cc_start: 0.3107 (OUTLIER) cc_final: 0.2470 (ptm-80) REVERT: B 3513 MET cc_start: 0.6515 (ptm) cc_final: 0.5990 (ptt) REVERT: B 3790 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7702 (p) REVERT: B 3794 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6991 (m-30) REVERT: B 4066 ILE cc_start: 0.8014 (mm) cc_final: 0.7701 (mm) REVERT: B 4201 MET cc_start: 0.6688 (ptp) cc_final: 0.6477 (ptp) REVERT: B 4229 ASN cc_start: 0.7007 (m110) cc_final: 0.6538 (t0) REVERT: B 4261 TYR cc_start: 0.8105 (p90) cc_final: 0.7806 (p90) REVERT: B 4370 ASP cc_start: 0.6356 (p0) cc_final: 0.6108 (m-30) outliers start: 215 outliers final: 143 residues processed: 475 average time/residue: 0.6823 time to fit residues: 574.0128 Evaluate side-chains 438 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 270 time to evaluate : 5.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 1104 HIS Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1384 ASN Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1840 THR Chi-restraints excluded: chain A residue 1871 VAL Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1931 GLU Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG Chi-restraints excluded: chain A residue 2176 ARG Chi-restraints excluded: chain A residue 2179 THR Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2453 TYR Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2544 VAL Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2596 SER Chi-restraints excluded: chain A residue 2692 TYR Chi-restraints excluded: chain A residue 2710 ASN Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2800 VAL Chi-restraints excluded: chain A residue 2990 CYS Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3020 CYS Chi-restraints excluded: chain A residue 3029 CYS Chi-restraints excluded: chain A residue 3079 LEU Chi-restraints excluded: chain A residue 3128 CYS Chi-restraints excluded: chain A residue 3136 TYR Chi-restraints excluded: chain A residue 3153 VAL Chi-restraints excluded: chain A residue 3205 PHE Chi-restraints excluded: chain A residue 3232 VAL Chi-restraints excluded: chain A residue 3265 THR Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3314 VAL Chi-restraints excluded: chain A residue 3315 ASP Chi-restraints excluded: chain A residue 3373 THR Chi-restraints excluded: chain A residue 3377 THR Chi-restraints excluded: chain A residue 3395 ASP Chi-restraints excluded: chain A residue 3400 HIS Chi-restraints excluded: chain A residue 3478 CYS Chi-restraints excluded: chain A residue 3497 ASP Chi-restraints excluded: chain A residue 3520 LEU Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3593 HIS Chi-restraints excluded: chain A residue 3594 HIS Chi-restraints excluded: chain A residue 3597 GLU Chi-restraints excluded: chain A residue 3621 CYS Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3729 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3777 ARG Chi-restraints excluded: chain A residue 3834 CYS Chi-restraints excluded: chain A residue 3970 ARG Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4268 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 905 ARG Chi-restraints excluded: chain B residue 947 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1291 CYS Chi-restraints excluded: chain B residue 1296 ASP Chi-restraints excluded: chain B residue 1378 LEU Chi-restraints excluded: chain B residue 1392 ILE Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1560 LEU Chi-restraints excluded: chain B residue 1610 ASN Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1698 GLN Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 1922 LEU Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2136 THR Chi-restraints excluded: chain B residue 2167 VAL Chi-restraints excluded: chain B residue 2171 LEU Chi-restraints excluded: chain B residue 2179 THR Chi-restraints excluded: chain B residue 2188 VAL Chi-restraints excluded: chain B residue 2242 MET Chi-restraints excluded: chain B residue 2440 LEU Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2699 THR Chi-restraints excluded: chain B residue 2713 CYS Chi-restraints excluded: chain B residue 2781 CYS Chi-restraints excluded: chain B residue 2938 ASP Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3220 SER Chi-restraints excluded: chain B residue 3256 MET Chi-restraints excluded: chain B residue 3290 ASP Chi-restraints excluded: chain B residue 3362 ILE Chi-restraints excluded: chain B residue 3417 ILE Chi-restraints excluded: chain B residue 3422 VAL Chi-restraints excluded: chain B residue 3501 THR Chi-restraints excluded: chain B residue 3507 ARG Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3554 PHE Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3788 ASP Chi-restraints excluded: chain B residue 3790 SER Chi-restraints excluded: chain B residue 3794 ASP Chi-restraints excluded: chain B residue 3972 CYS Chi-restraints excluded: chain B residue 3982 THR Chi-restraints excluded: chain B residue 4136 VAL Chi-restraints excluded: chain B residue 4268 LEU Chi-restraints excluded: chain B residue 4312 VAL Chi-restraints excluded: chain B residue 4365 SER Chi-restraints excluded: chain B residue 4373 SER Chi-restraints excluded: chain B residue 4375 LEU Chi-restraints excluded: chain I residue 3 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 802 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 474 optimal weight: 9.9990 chunk 607 optimal weight: 0.9990 chunk 470 optimal weight: 20.0000 chunk 700 optimal weight: 0.1980 chunk 464 optimal weight: 20.0000 chunk 828 optimal weight: 20.0000 chunk 518 optimal weight: 7.9990 chunk 505 optimal weight: 0.0470 chunk 382 optimal weight: 8.9990 overall best weight: 2.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1312 HIS A2710 ASN A3782 GLN ** A3789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2989 ASN ** B3042 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 71548 Z= 0.205 Angle : 0.594 10.350 97174 Z= 0.307 Chirality : 0.046 0.434 10764 Planarity : 0.004 0.087 12770 Dihedral : 6.984 68.241 12952 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.71 % Allowed : 15.75 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.09), residues: 8608 helix: -3.13 (0.29), residues: 161 sheet: -0.82 (0.10), residues: 2346 loop : -0.58 (0.08), residues: 6101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 844 HIS 0.005 0.001 HIS A3594 PHE 0.034 0.001 PHE A4033 TYR 0.024 0.001 TYR A4079 ARG 0.006 0.000 ARG A4176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 287 time to evaluate : 5.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6650 (mt0) REVERT: A 308 MET cc_start: 0.5293 (mmt) cc_final: 0.4795 (tmm) REVERT: A 666 ASN cc_start: 0.6211 (OUTLIER) cc_final: 0.5879 (t0) REVERT: A 1215 ARG cc_start: 0.6661 (tpp-160) cc_final: 0.6047 (mmp-170) REVERT: A 1654 ASP cc_start: 0.7201 (m-30) cc_final: 0.6828 (t70) REVERT: A 1737 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8615 (p0) REVERT: A 1829 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8382 (tt) REVERT: A 2079 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7800 (mm) REVERT: A 2088 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8554 (ptm) REVERT: A 2127 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7429 (ptp-170) REVERT: A 2176 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7124 (mmm-85) REVERT: A 2320 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8601 (mptp) REVERT: A 2378 ASN cc_start: 0.8506 (p0) cc_final: 0.8096 (m110) REVERT: A 2426 ASP cc_start: 0.8703 (t0) cc_final: 0.8428 (t0) REVERT: A 2453 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: A 2702 ASN cc_start: 0.8197 (t0) cc_final: 0.7985 (t0) REVERT: A 2990 CYS cc_start: 0.5337 (OUTLIER) cc_final: 0.5121 (t) REVERT: A 3029 CYS cc_start: 0.5219 (OUTLIER) cc_final: 0.4800 (p) REVERT: A 3205 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.5683 (t80) REVERT: A 3235 ASP cc_start: 0.8094 (t0) cc_final: 0.7461 (t0) REVERT: A 3240 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7041 (tt0) REVERT: A 3249 GLU cc_start: 0.8127 (tt0) cc_final: 0.7674 (tm-30) REVERT: A 3270 ARG cc_start: 0.7728 (tpp-160) cc_final: 0.7256 (tpp-160) REVERT: A 3395 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6424 (p0) REVERT: A 3433 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7174 (mp0) REVERT: A 3760 GLU cc_start: 0.7108 (pm20) cc_final: 0.6506 (mm-30) REVERT: A 3876 GLU cc_start: 0.5121 (mm-30) cc_final: 0.4662 (pt0) REVERT: A 4144 MET cc_start: 0.6992 (mmm) cc_final: 0.6660 (mmm) REVERT: A 4201 MET cc_start: 0.5637 (mtm) cc_final: 0.5132 (mmm) REVERT: A 4216 TRP cc_start: 0.6098 (m-10) cc_final: 0.5867 (m-10) REVERT: A 4274 MET cc_start: 0.6346 (ptp) cc_final: 0.6025 (pmm) REVERT: A 4360 ASP cc_start: 0.8376 (t0) cc_final: 0.7713 (m-30) REVERT: A 4370 ASP cc_start: 0.5568 (p0) cc_final: 0.5208 (m-30) REVERT: B 257 GLU cc_start: 0.7546 (mp0) cc_final: 0.7206 (pm20) REVERT: B 426 MET cc_start: 0.6582 (tpt) cc_final: 0.6285 (tpt) REVERT: B 856 ASP cc_start: 0.8357 (m-30) cc_final: 0.7995 (m-30) REVERT: B 905 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7497 (ttt180) REVERT: B 957 MET cc_start: 0.7980 (mmt) cc_final: 0.7566 (mmm) REVERT: B 1003 MET cc_start: 0.7002 (mtm) cc_final: 0.6518 (mpp) REVERT: B 1010 MET cc_start: 0.6983 (mtt) cc_final: 0.6536 (mtt) REVERT: B 1034 ASN cc_start: 0.5914 (t0) cc_final: 0.5429 (p0) REVERT: B 1088 ARG cc_start: 0.7508 (mmt90) cc_final: 0.7050 (tmm160) REVERT: B 1215 ARG cc_start: 0.7753 (tpm170) cc_final: 0.7377 (mtm110) REVERT: B 1560 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7496 (pp) REVERT: B 1698 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8124 (mm-40) REVERT: B 2179 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7851 (p) REVERT: B 2225 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8463 (t0) REVERT: B 2562 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8558 (tp30) REVERT: B 2938 ASP cc_start: 0.0198 (OUTLIER) cc_final: -0.0366 (t0) REVERT: B 3308 MET cc_start: 0.8073 (ptm) cc_final: 0.7587 (tmm) REVERT: B 3507 ARG cc_start: 0.3048 (OUTLIER) cc_final: 0.2424 (ptm-80) REVERT: B 3790 SER cc_start: 0.8072 (OUTLIER) cc_final: 0.7708 (p) REVERT: B 3794 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7000 (m-30) REVERT: B 4066 ILE cc_start: 0.8017 (mm) cc_final: 0.7685 (mm) REVERT: B 4201 MET cc_start: 0.6527 (ptp) cc_final: 0.6267 (ptp) REVERT: B 4217 MET cc_start: 0.5595 (tpt) cc_final: 0.5190 (tpp) REVERT: B 4229 ASN cc_start: 0.6977 (m110) cc_final: 0.6555 (t0) REVERT: B 4232 TRP cc_start: 0.7936 (m-10) cc_final: 0.7548 (m-90) REVERT: B 4261 TYR cc_start: 0.8138 (p90) cc_final: 0.7852 (p90) REVERT: B 4370 ASP cc_start: 0.6361 (p0) cc_final: 0.6120 (m-30) outliers start: 206 outliers final: 147 residues processed: 469 average time/residue: 0.6332 time to fit residues: 527.0402 Evaluate side-chains 434 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 264 time to evaluate : 5.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1104 HIS Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1384 ASN Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1515 ILE Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1602 CYS Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1829 LEU Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1871 VAL Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1931 GLU Chi-restraints excluded: chain A residue 1974 LEU Chi-restraints excluded: chain A residue 2031 GLN Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG Chi-restraints excluded: chain A residue 2176 ARG Chi-restraints excluded: chain A residue 2179 THR Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2453 TYR Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2544 VAL Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2596 SER Chi-restraints excluded: chain A residue 2692 TYR Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2800 VAL Chi-restraints excluded: chain A residue 2990 CYS Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3020 CYS Chi-restraints excluded: chain A residue 3029 CYS Chi-restraints excluded: chain A residue 3079 LEU Chi-restraints excluded: chain A residue 3094 ARG Chi-restraints excluded: chain A residue 3128 CYS Chi-restraints excluded: chain A residue 3136 TYR Chi-restraints excluded: chain A residue 3153 VAL Chi-restraints excluded: chain A residue 3205 PHE Chi-restraints excluded: chain A residue 3265 THR Chi-restraints excluded: chain A residue 3269 HIS Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3314 VAL Chi-restraints excluded: chain A residue 3315 ASP Chi-restraints excluded: chain A residue 3373 THR Chi-restraints excluded: chain A residue 3377 THR Chi-restraints excluded: chain A residue 3395 ASP Chi-restraints excluded: chain A residue 3400 HIS Chi-restraints excluded: chain A residue 3478 CYS Chi-restraints excluded: chain A residue 3497 ASP Chi-restraints excluded: chain A residue 3520 LEU Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3593 HIS Chi-restraints excluded: chain A residue 3597 GLU Chi-restraints excluded: chain A residue 3621 CYS Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3729 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3834 CYS Chi-restraints excluded: chain A residue 3881 PHE Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4268 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 905 ARG Chi-restraints excluded: chain B residue 947 THR Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1291 CYS Chi-restraints excluded: chain B residue 1296 ASP Chi-restraints excluded: chain B residue 1378 LEU Chi-restraints excluded: chain B residue 1392 ILE Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1560 LEU Chi-restraints excluded: chain B residue 1610 ASN Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1698 GLN Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 1922 LEU Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2136 THR Chi-restraints excluded: chain B residue 2167 VAL Chi-restraints excluded: chain B residue 2179 THR Chi-restraints excluded: chain B residue 2188 VAL Chi-restraints excluded: chain B residue 2225 ASN Chi-restraints excluded: chain B residue 2242 MET Chi-restraints excluded: chain B residue 2280 THR Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2440 LEU Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2713 CYS Chi-restraints excluded: chain B residue 2781 CYS Chi-restraints excluded: chain B residue 2938 ASP Chi-restraints excluded: chain B residue 3035 HIS Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3220 SER Chi-restraints excluded: chain B residue 3256 MET Chi-restraints excluded: chain B residue 3290 ASP Chi-restraints excluded: chain B residue 3362 ILE Chi-restraints excluded: chain B residue 3417 ILE Chi-restraints excluded: chain B residue 3422 VAL Chi-restraints excluded: chain B residue 3501 THR Chi-restraints excluded: chain B residue 3507 ARG Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3553 ARG Chi-restraints excluded: chain B residue 3554 PHE Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3788 ASP Chi-restraints excluded: chain B residue 3790 SER Chi-restraints excluded: chain B residue 3794 ASP Chi-restraints excluded: chain B residue 3972 CYS Chi-restraints excluded: chain B residue 4108 LEU Chi-restraints excluded: chain B residue 4136 VAL Chi-restraints excluded: chain B residue 4268 LEU Chi-restraints excluded: chain B residue 4312 VAL Chi-restraints excluded: chain B residue 4365 SER Chi-restraints excluded: chain B residue 4373 SER Chi-restraints excluded: chain B residue 4375 LEU Chi-restraints excluded: chain I residue 3 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 512 optimal weight: 8.9990 chunk 331 optimal weight: 6.9990 chunk 495 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 526 optimal weight: 9.9990 chunk 564 optimal weight: 0.9980 chunk 409 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 651 optimal weight: 0.0870 overall best weight: 3.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 GLN A1312 HIS ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3080 HIS A3552 HIS ** A3789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3921 HIS ** A3979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1367 GLN B1610 ASN ** B2871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3042 GLN ** B3336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 71548 Z= 0.289 Angle : 0.639 10.429 97174 Z= 0.329 Chirality : 0.047 0.437 10764 Planarity : 0.005 0.067 12770 Dihedral : 7.173 69.917 12951 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.87 % Allowed : 15.85 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.09), residues: 8608 helix: -3.27 (0.27), residues: 167 sheet: -0.95 (0.10), residues: 2352 loop : -0.63 (0.08), residues: 6089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 270 HIS 0.007 0.001 HIS A 958 PHE 0.027 0.002 PHE A4033 TYR 0.021 0.002 TYR B1622 ARG 0.010 0.001 ARG A3970 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 270 time to evaluate : 5.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6542 (mt0) REVERT: A 308 MET cc_start: 0.5767 (mmt) cc_final: 0.5376 (tmm) REVERT: A 368 HIS cc_start: 0.2447 (OUTLIER) cc_final: 0.2069 (p-80) REVERT: A 1215 ARG cc_start: 0.6528 (tpp-160) cc_final: 0.5928 (mmp-170) REVERT: A 1737 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8583 (p0) REVERT: A 1755 ASN cc_start: 0.8053 (t0) cc_final: 0.7443 (t0) REVERT: A 1829 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8469 (tt) REVERT: A 1856 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7474 (mmp80) REVERT: A 2079 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7765 (mm) REVERT: A 2088 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8568 (ptm) REVERT: A 2127 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7400 (ptp-170) REVERT: A 2320 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8703 (mptp) REVERT: A 2453 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: A 2990 CYS cc_start: 0.5573 (OUTLIER) cc_final: 0.5364 (t) REVERT: A 3029 CYS cc_start: 0.5047 (OUTLIER) cc_final: 0.4295 (p) REVERT: A 3145 LEU cc_start: 0.4991 (OUTLIER) cc_final: 0.4582 (tp) REVERT: A 3205 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.5459 (t80) REVERT: A 3235 ASP cc_start: 0.8043 (t0) cc_final: 0.7494 (t0) REVERT: A 3240 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7019 (mt-10) REVERT: A 3249 GLU cc_start: 0.8164 (tt0) cc_final: 0.7733 (tm-30) REVERT: A 3270 ARG cc_start: 0.7703 (tpp-160) cc_final: 0.7285 (tpp-160) REVERT: A 3395 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6389 (p0) REVERT: A 3433 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7168 (mp0) REVERT: A 3760 GLU cc_start: 0.7057 (pm20) cc_final: 0.6332 (mm-30) REVERT: A 3854 HIS cc_start: 0.6556 (m90) cc_final: 0.6295 (m90) REVERT: A 4067 ARG cc_start: 0.7695 (mtp180) cc_final: 0.7289 (mmm160) REVERT: A 4079 TYR cc_start: 0.6657 (t80) cc_final: 0.6375 (t80) REVERT: A 4144 MET cc_start: 0.6850 (mmm) cc_final: 0.6562 (mmm) REVERT: A 4216 TRP cc_start: 0.6185 (m-10) cc_final: 0.5940 (m-10) REVERT: A 4217 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.5082 (mmt) REVERT: A 4260 LYS cc_start: 0.7030 (tptp) cc_final: 0.6637 (mmmt) REVERT: A 4274 MET cc_start: 0.6503 (ptp) cc_final: 0.6163 (pmm) REVERT: A 4360 ASP cc_start: 0.8499 (t0) cc_final: 0.7705 (m-30) REVERT: A 4370 ASP cc_start: 0.5436 (p0) cc_final: 0.5005 (m-30) REVERT: B 257 GLU cc_start: 0.7550 (mp0) cc_final: 0.7201 (pm20) REVERT: B 426 MET cc_start: 0.6651 (tpt) cc_final: 0.6340 (tpt) REVERT: B 856 ASP cc_start: 0.8562 (m-30) cc_final: 0.8230 (m-30) REVERT: B 905 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7451 (ttt180) REVERT: B 957 MET cc_start: 0.8033 (mmt) cc_final: 0.7576 (mmp) REVERT: B 1003 MET cc_start: 0.6997 (mtm) cc_final: 0.6469 (mpp) REVERT: B 1010 MET cc_start: 0.6947 (mtt) cc_final: 0.6452 (mtt) REVERT: B 1034 ASN cc_start: 0.5959 (t0) cc_final: 0.5484 (p0) REVERT: B 1088 ARG cc_start: 0.7561 (mmt90) cc_final: 0.7015 (tmm160) REVERT: B 1215 ARG cc_start: 0.7784 (tpm170) cc_final: 0.7220 (mtm110) REVERT: B 1258 ILE cc_start: 0.9036 (tt) cc_final: 0.8786 (pt) REVERT: B 1560 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7464 (pp) REVERT: B 1698 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8080 (mm-40) REVERT: B 1750 MET cc_start: 0.8626 (mtm) cc_final: 0.8243 (mtp) REVERT: B 1847 GLU cc_start: 0.8683 (mt-10) cc_final: 0.7842 (mt-10) REVERT: B 2179 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7807 (p) REVERT: B 2225 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8361 (t0) REVERT: B 2562 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8566 (tp30) REVERT: B 2938 ASP cc_start: -0.0003 (OUTLIER) cc_final: -0.0599 (t0) REVERT: B 3220 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.8170 (p) REVERT: B 3308 MET cc_start: 0.7987 (ptm) cc_final: 0.7518 (tmm) REVERT: B 3507 ARG cc_start: 0.3702 (OUTLIER) cc_final: 0.3084 (ptm-80) REVERT: B 3511 MET cc_start: 0.7057 (ppp) cc_final: 0.6762 (mtm) REVERT: B 3790 SER cc_start: 0.7640 (OUTLIER) cc_final: 0.7318 (p) REVERT: B 3794 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7124 (m-30) REVERT: B 4011 ASN cc_start: 0.5370 (t0) cc_final: 0.4929 (m-40) REVERT: B 4201 MET cc_start: 0.6824 (ptp) cc_final: 0.6532 (ptp) REVERT: B 4217 MET cc_start: 0.5704 (tpt) cc_final: 0.5457 (tpp) REVERT: B 4229 ASN cc_start: 0.7038 (m110) cc_final: 0.6627 (t0) REVERT: B 4232 TRP cc_start: 0.7933 (m-10) cc_final: 0.7562 (m-90) REVERT: B 4268 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6386 (tt) REVERT: B 4379 MET cc_start: 0.4367 (mmt) cc_final: 0.3992 (mmt) outliers start: 218 outliers final: 154 residues processed: 467 average time/residue: 0.7096 time to fit residues: 586.2925 Evaluate side-chains 437 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 256 time to evaluate : 5.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1162 CYS Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1384 ASN Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1515 ILE Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1602 CYS Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1829 LEU Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1840 THR Chi-restraints excluded: chain A residue 1856 ARG Chi-restraints excluded: chain A residue 1871 VAL Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1931 GLU Chi-restraints excluded: chain A residue 2031 GLN Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2066 MET Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG Chi-restraints excluded: chain A residue 2179 THR Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2254 ASP Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2453 TYR Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2544 VAL Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2596 SER Chi-restraints excluded: chain A residue 2692 TYR Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2800 VAL Chi-restraints excluded: chain A residue 2990 CYS Chi-restraints excluded: chain A residue 3020 CYS Chi-restraints excluded: chain A residue 3029 CYS Chi-restraints excluded: chain A residue 3079 LEU Chi-restraints excluded: chain A residue 3128 CYS Chi-restraints excluded: chain A residue 3136 TYR Chi-restraints excluded: chain A residue 3145 LEU Chi-restraints excluded: chain A residue 3153 VAL Chi-restraints excluded: chain A residue 3205 PHE Chi-restraints excluded: chain A residue 3232 VAL Chi-restraints excluded: chain A residue 3265 THR Chi-restraints excluded: chain A residue 3269 HIS Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3314 VAL Chi-restraints excluded: chain A residue 3315 ASP Chi-restraints excluded: chain A residue 3373 THR Chi-restraints excluded: chain A residue 3377 THR Chi-restraints excluded: chain A residue 3395 ASP Chi-restraints excluded: chain A residue 3400 HIS Chi-restraints excluded: chain A residue 3478 CYS Chi-restraints excluded: chain A residue 3520 LEU Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3593 HIS Chi-restraints excluded: chain A residue 3594 HIS Chi-restraints excluded: chain A residue 3597 GLU Chi-restraints excluded: chain A residue 3621 CYS Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3729 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3777 ARG Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4268 LEU Chi-restraints excluded: chain A residue 4306 ASN Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 905 ARG Chi-restraints excluded: chain B residue 947 THR Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1291 CYS Chi-restraints excluded: chain B residue 1296 ASP Chi-restraints excluded: chain B residue 1378 LEU Chi-restraints excluded: chain B residue 1392 ILE Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1560 LEU Chi-restraints excluded: chain B residue 1610 ASN Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1681 MET Chi-restraints excluded: chain B residue 1698 GLN Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 1922 LEU Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2136 THR Chi-restraints excluded: chain B residue 2167 VAL Chi-restraints excluded: chain B residue 2171 LEU Chi-restraints excluded: chain B residue 2179 THR Chi-restraints excluded: chain B residue 2188 VAL Chi-restraints excluded: chain B residue 2225 ASN Chi-restraints excluded: chain B residue 2280 THR Chi-restraints excluded: chain B residue 2327 VAL Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2440 LEU Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2699 THR Chi-restraints excluded: chain B residue 2713 CYS Chi-restraints excluded: chain B residue 2781 CYS Chi-restraints excluded: chain B residue 2938 ASP Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3220 SER Chi-restraints excluded: chain B residue 3256 MET Chi-restraints excluded: chain B residue 3290 ASP Chi-restraints excluded: chain B residue 3362 ILE Chi-restraints excluded: chain B residue 3388 LEU Chi-restraints excluded: chain B residue 3417 ILE Chi-restraints excluded: chain B residue 3422 VAL Chi-restraints excluded: chain B residue 3507 ARG Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3553 ARG Chi-restraints excluded: chain B residue 3554 PHE Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3788 ASP Chi-restraints excluded: chain B residue 3790 SER Chi-restraints excluded: chain B residue 3794 ASP Chi-restraints excluded: chain B residue 3972 CYS Chi-restraints excluded: chain B residue 4108 LEU Chi-restraints excluded: chain B residue 4136 VAL Chi-restraints excluded: chain B residue 4268 LEU Chi-restraints excluded: chain B residue 4312 VAL Chi-restraints excluded: chain B residue 4365 SER Chi-restraints excluded: chain B residue 4373 SER Chi-restraints excluded: chain B residue 4375 LEU Chi-restraints excluded: chain I residue 3 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 754 optimal weight: 0.0070 chunk 794 optimal weight: 2.9990 chunk 724 optimal weight: 10.0000 chunk 772 optimal weight: 5.9990 chunk 793 optimal weight: 8.9990 chunk 464 optimal weight: 20.0000 chunk 336 optimal weight: 0.0370 chunk 606 optimal weight: 0.7980 chunk 237 optimal weight: 10.0000 chunk 698 optimal weight: 4.9990 chunk 730 optimal weight: 7.9990 overall best weight: 1.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN A 780 ASN A1312 HIS ** A3789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1610 ASN ** B2871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3983 GLN ** B4299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 71548 Z= 0.190 Angle : 0.592 10.520 97174 Z= 0.305 Chirality : 0.046 0.425 10764 Planarity : 0.004 0.084 12770 Dihedral : 6.882 65.951 12951 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.37 % Allowed : 16.43 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.09), residues: 8608 helix: -3.05 (0.29), residues: 167 sheet: -0.85 (0.10), residues: 2346 loop : -0.59 (0.08), residues: 6095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1483 HIS 0.013 0.001 HIS A4324 PHE 0.026 0.001 PHE A4033 TYR 0.016 0.001 TYR A3209 ARG 0.016 0.000 ARG A3094 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 278 time to evaluate : 5.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6533 (mt0) REVERT: A 308 MET cc_start: 0.5487 (mmt) cc_final: 0.5060 (tmm) REVERT: A 729 GLU cc_start: 0.5864 (mm-30) cc_final: 0.5552 (mm-30) REVERT: A 1215 ARG cc_start: 0.6509 (tpp-160) cc_final: 0.5915 (mmp-170) REVERT: A 1737 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8605 (p0) REVERT: A 1829 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8359 (tt) REVERT: A 1856 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7436 (mmp80) REVERT: A 2079 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7788 (mm) REVERT: A 2088 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8510 (ptm) REVERT: A 2127 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7460 (ptp-170) REVERT: A 2242 MET cc_start: 0.8498 (tpt) cc_final: 0.8077 (tpt) REVERT: A 2320 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8601 (mptp) REVERT: A 2378 ASN cc_start: 0.8307 (p0) cc_final: 0.7883 (m110) REVERT: A 2453 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: A 2990 CYS cc_start: 0.5563 (OUTLIER) cc_final: 0.5356 (t) REVERT: A 3145 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5449 (tp) REVERT: A 3205 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.5494 (t80) REVERT: A 3235 ASP cc_start: 0.7996 (t0) cc_final: 0.7431 (t0) REVERT: A 3240 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7056 (tt0) REVERT: A 3249 GLU cc_start: 0.8094 (tt0) cc_final: 0.7706 (tm-30) REVERT: A 3270 ARG cc_start: 0.7645 (tpp-160) cc_final: 0.7325 (tpp-160) REVERT: A 3433 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7161 (mp0) REVERT: A 3497 ASP cc_start: 0.7460 (p0) cc_final: 0.7128 (m-30) REVERT: A 3760 GLU cc_start: 0.7059 (pm20) cc_final: 0.6333 (mm-30) REVERT: A 3854 HIS cc_start: 0.6720 (m90) cc_final: 0.6366 (m90) REVERT: A 3876 GLU cc_start: 0.5164 (mm-30) cc_final: 0.4715 (pt0) REVERT: A 4144 MET cc_start: 0.7009 (mmm) cc_final: 0.6729 (mmm) REVERT: A 4201 MET cc_start: 0.6219 (mtm) cc_final: 0.5810 (mmm) REVERT: A 4274 MET cc_start: 0.6528 (ptp) cc_final: 0.6182 (pmm) REVERT: A 4360 ASP cc_start: 0.8493 (t0) cc_final: 0.7700 (m-30) REVERT: A 4370 ASP cc_start: 0.5541 (p0) cc_final: 0.5214 (m-30) REVERT: B 257 GLU cc_start: 0.7574 (mp0) cc_final: 0.7245 (pm20) REVERT: B 426 MET cc_start: 0.6658 (tpt) cc_final: 0.6353 (tpt) REVERT: B 856 ASP cc_start: 0.8482 (m-30) cc_final: 0.8177 (m-30) REVERT: B 905 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7454 (ttt180) REVERT: B 916 PHE cc_start: 0.8354 (t80) cc_final: 0.7776 (t80) REVERT: B 957 MET cc_start: 0.8053 (mmt) cc_final: 0.7564 (mmm) REVERT: B 1003 MET cc_start: 0.7009 (mtm) cc_final: 0.6529 (mpp) REVERT: B 1010 MET cc_start: 0.7064 (mtt) cc_final: 0.6618 (mtt) REVERT: B 1034 ASN cc_start: 0.6019 (t0) cc_final: 0.5569 (p0) REVERT: B 1088 ARG cc_start: 0.7558 (mmt90) cc_final: 0.7019 (tmm160) REVERT: B 1215 ARG cc_start: 0.7792 (tpm170) cc_final: 0.7224 (mtm110) REVERT: B 1258 ILE cc_start: 0.9030 (tt) cc_final: 0.8786 (pt) REVERT: B 1560 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7445 (pp) REVERT: B 1698 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8116 (mm-40) REVERT: B 2179 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7922 (p) REVERT: B 2225 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8420 (t0) REVERT: B 2562 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8542 (tp30) REVERT: B 2938 ASP cc_start: 0.0026 (OUTLIER) cc_final: -0.0569 (t0) REVERT: B 3092 MET cc_start: 0.3288 (mmt) cc_final: 0.2605 (mtt) REVERT: B 3220 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.8204 (p) REVERT: B 3308 MET cc_start: 0.7978 (ptm) cc_final: 0.7490 (tmm) REVERT: B 3507 ARG cc_start: 0.3676 (OUTLIER) cc_final: 0.3041 (ptm-80) REVERT: B 3511 MET cc_start: 0.7596 (ppp) cc_final: 0.7379 (mtm) REVERT: B 3513 MET cc_start: 0.6364 (ptt) cc_final: 0.5937 (ptt) REVERT: B 3790 SER cc_start: 0.7615 (OUTLIER) cc_final: 0.7330 (p) REVERT: B 3794 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7055 (m-30) REVERT: B 4011 ASN cc_start: 0.4683 (t0) cc_final: 0.4076 (m-40) REVERT: B 4201 MET cc_start: 0.6819 (ptp) cc_final: 0.6573 (ptp) REVERT: B 4229 ASN cc_start: 0.7012 (m110) cc_final: 0.6628 (t0) REVERT: B 4232 TRP cc_start: 0.7925 (m-10) cc_final: 0.7549 (m-90) REVERT: B 4379 MET cc_start: 0.4276 (mmt) cc_final: 0.4065 (mmt) outliers start: 180 outliers final: 136 residues processed: 437 average time/residue: 0.6638 time to fit residues: 515.8422 Evaluate side-chains 419 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 261 time to evaluate : 5.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1162 CYS Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1384 ASN Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1602 CYS Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1829 LEU Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1840 THR Chi-restraints excluded: chain A residue 1856 ARG Chi-restraints excluded: chain A residue 1919 LEU Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1931 GLU Chi-restraints excluded: chain A residue 2031 GLN Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2254 ASP Chi-restraints excluded: chain A residue 2320 LYS Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2453 TYR Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2544 VAL Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2596 SER Chi-restraints excluded: chain A residue 2686 LEU Chi-restraints excluded: chain A residue 2692 TYR Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2800 VAL Chi-restraints excluded: chain A residue 2990 CYS Chi-restraints excluded: chain A residue 3020 CYS Chi-restraints excluded: chain A residue 3029 CYS Chi-restraints excluded: chain A residue 3128 CYS Chi-restraints excluded: chain A residue 3136 TYR Chi-restraints excluded: chain A residue 3145 LEU Chi-restraints excluded: chain A residue 3153 VAL Chi-restraints excluded: chain A residue 3205 PHE Chi-restraints excluded: chain A residue 3232 VAL Chi-restraints excluded: chain A residue 3265 THR Chi-restraints excluded: chain A residue 3269 HIS Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3314 VAL Chi-restraints excluded: chain A residue 3315 ASP Chi-restraints excluded: chain A residue 3377 THR Chi-restraints excluded: chain A residue 3400 HIS Chi-restraints excluded: chain A residue 3478 CYS Chi-restraints excluded: chain A residue 3520 LEU Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3593 HIS Chi-restraints excluded: chain A residue 3594 HIS Chi-restraints excluded: chain A residue 3597 GLU Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3729 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4268 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 905 ARG Chi-restraints excluded: chain B residue 947 THR Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1291 CYS Chi-restraints excluded: chain B residue 1296 ASP Chi-restraints excluded: chain B residue 1378 LEU Chi-restraints excluded: chain B residue 1392 ILE Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1560 LEU Chi-restraints excluded: chain B residue 1589 MET Chi-restraints excluded: chain B residue 1610 ASN Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1698 GLN Chi-restraints excluded: chain B residue 1827 LEU Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 1922 LEU Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 2005 LEU Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2167 VAL Chi-restraints excluded: chain B residue 2173 GLU Chi-restraints excluded: chain B residue 2179 THR Chi-restraints excluded: chain B residue 2188 VAL Chi-restraints excluded: chain B residue 2225 ASN Chi-restraints excluded: chain B residue 2280 THR Chi-restraints excluded: chain B residue 2327 VAL Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2699 THR Chi-restraints excluded: chain B residue 2713 CYS Chi-restraints excluded: chain B residue 2938 ASP Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3220 SER Chi-restraints excluded: chain B residue 3256 MET Chi-restraints excluded: chain B residue 3290 ASP Chi-restraints excluded: chain B residue 3362 ILE Chi-restraints excluded: chain B residue 3417 ILE Chi-restraints excluded: chain B residue 3422 VAL Chi-restraints excluded: chain B residue 3431 THR Chi-restraints excluded: chain B residue 3507 ARG Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3553 ARG Chi-restraints excluded: chain B residue 3554 PHE Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3788 ASP Chi-restraints excluded: chain B residue 3790 SER Chi-restraints excluded: chain B residue 3794 ASP Chi-restraints excluded: chain B residue 3952 VAL Chi-restraints excluded: chain B residue 3982 THR Chi-restraints excluded: chain B residue 4108 LEU Chi-restraints excluded: chain B residue 4136 VAL Chi-restraints excluded: chain B residue 4261 TYR Chi-restraints excluded: chain B residue 4268 LEU Chi-restraints excluded: chain B residue 4312 VAL Chi-restraints excluded: chain B residue 4365 SER Chi-restraints excluded: chain B residue 4375 LEU Chi-restraints excluded: chain I residue 3 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 769 optimal weight: 0.2980 chunk 507 optimal weight: 0.8980 chunk 816 optimal weight: 20.0000 chunk 498 optimal weight: 9.9990 chunk 387 optimal weight: 0.9990 chunk 567 optimal weight: 0.9980 chunk 856 optimal weight: 4.9990 chunk 788 optimal weight: 10.0000 chunk 682 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 526 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 ASN A1312 HIS ** A2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3378 ASN A3782 GLN A3789 ASN ** A3979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3336 HIS B3732 HIS ** B3804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 71548 Z= 0.153 Angle : 0.579 17.310 97174 Z= 0.297 Chirality : 0.046 0.438 10764 Planarity : 0.004 0.064 12770 Dihedral : 6.550 61.326 12948 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.88 % Allowed : 16.90 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.09), residues: 8608 helix: -2.94 (0.30), residues: 179 sheet: -0.73 (0.11), residues: 2300 loop : -0.55 (0.08), residues: 6129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A4216 HIS 0.006 0.001 HIS A4324 PHE 0.021 0.001 PHE B1155 TYR 0.026 0.001 TYR A4247 ARG 0.012 0.000 ARG A3094 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17216 Ramachandran restraints generated. 8608 Oldfield, 0 Emsley, 8608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 286 time to evaluate : 5.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6466 (mt0) REVERT: A 308 MET cc_start: 0.5645 (mmt) cc_final: 0.5116 (tmm) REVERT: A 729 GLU cc_start: 0.6011 (mm-30) cc_final: 0.5740 (mm-30) REVERT: A 1215 ARG cc_start: 0.6505 (tpp-160) cc_final: 0.5915 (mmp-170) REVERT: A 1737 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8619 (p0) REVERT: A 1755 ASN cc_start: 0.7896 (t0) cc_final: 0.7312 (t0) REVERT: A 1829 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8290 (tt) REVERT: A 1856 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7388 (mmp80) REVERT: A 1931 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7957 (tp30) REVERT: A 2079 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7754 (mm) REVERT: A 2088 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8522 (ptm) REVERT: A 2127 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.7556 (ptp-170) REVERT: A 2242 MET cc_start: 0.8427 (tpt) cc_final: 0.8040 (tpt) REVERT: A 2378 ASN cc_start: 0.8309 (p0) cc_final: 0.7904 (m110) REVERT: A 2453 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: A 2990 CYS cc_start: 0.5564 (OUTLIER) cc_final: 0.5356 (t) REVERT: A 3145 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5442 (tp) REVERT: A 3205 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.5123 (t80) REVERT: A 3235 ASP cc_start: 0.8042 (t0) cc_final: 0.7387 (t0) REVERT: A 3240 GLU cc_start: 0.7285 (mt-10) cc_final: 0.7029 (tt0) REVERT: A 3249 GLU cc_start: 0.8103 (tt0) cc_final: 0.7708 (tm-30) REVERT: A 3270 ARG cc_start: 0.7745 (tpp-160) cc_final: 0.7437 (tpp-160) REVERT: A 3381 LEU cc_start: 0.8803 (mt) cc_final: 0.8242 (mp) REVERT: A 3760 GLU cc_start: 0.7092 (pm20) cc_final: 0.6393 (mm-30) REVERT: A 4144 MET cc_start: 0.6945 (mmm) cc_final: 0.6663 (mmm) REVERT: A 4201 MET cc_start: 0.6082 (mtm) cc_final: 0.5798 (mmm) REVERT: A 4239 ASP cc_start: 0.6540 (t0) cc_final: 0.6316 (t70) REVERT: A 4274 MET cc_start: 0.6875 (ptp) cc_final: 0.6432 (pmm) REVERT: A 4360 ASP cc_start: 0.8376 (t0) cc_final: 0.7652 (m-30) REVERT: A 4370 ASP cc_start: 0.5510 (p0) cc_final: 0.5215 (m-30) REVERT: B 257 GLU cc_start: 0.7530 (mp0) cc_final: 0.7201 (pm20) REVERT: B 426 MET cc_start: 0.6900 (tpt) cc_final: 0.6640 (tpt) REVERT: B 624 MET cc_start: 0.3295 (mtt) cc_final: 0.3086 (mtm) REVERT: B 856 ASP cc_start: 0.8306 (m-30) cc_final: 0.7962 (m-30) REVERT: B 905 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7557 (ttt180) REVERT: B 916 PHE cc_start: 0.8255 (t80) cc_final: 0.8014 (t80) REVERT: B 957 MET cc_start: 0.8014 (mmt) cc_final: 0.7474 (mmm) REVERT: B 1003 MET cc_start: 0.7092 (mtm) cc_final: 0.6590 (mpp) REVERT: B 1010 MET cc_start: 0.6867 (mtt) cc_final: 0.6377 (mtt) REVERT: B 1034 ASN cc_start: 0.6019 (t0) cc_final: 0.5532 (p0) REVERT: B 1088 ARG cc_start: 0.7540 (mmt90) cc_final: 0.7099 (tmm160) REVERT: B 1215 ARG cc_start: 0.7807 (tpm170) cc_final: 0.7220 (mtm110) REVERT: B 1258 ILE cc_start: 0.8891 (tt) cc_final: 0.8650 (pt) REVERT: B 1560 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7546 (pp) REVERT: B 1698 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8002 (mm-40) REVERT: B 1750 MET cc_start: 0.8387 (mtm) cc_final: 0.7928 (mtm) REVERT: B 2173 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: B 2179 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7881 (p) REVERT: B 2562 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8532 (tp30) REVERT: B 3092 MET cc_start: 0.3553 (mmt) cc_final: 0.2976 (mtt) REVERT: B 3220 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.8214 (p) REVERT: B 3308 MET cc_start: 0.7963 (ptm) cc_final: 0.7244 (tmm) REVERT: B 3507 ARG cc_start: 0.3688 (OUTLIER) cc_final: 0.3060 (ptm-80) REVERT: B 3790 SER cc_start: 0.7742 (OUTLIER) cc_final: 0.7512 (p) REVERT: B 3794 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7061 (m-30) REVERT: B 4011 ASN cc_start: 0.4694 (t0) cc_final: 0.4098 (m-40) REVERT: B 4229 ASN cc_start: 0.6922 (m110) cc_final: 0.6566 (t0) REVERT: B 4232 TRP cc_start: 0.7969 (m-10) cc_final: 0.7600 (m-90) REVERT: B 4268 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6601 (tt) REVERT: B 4379 MET cc_start: 0.4428 (mmt) cc_final: 0.4186 (mmt) outliers start: 143 outliers final: 109 residues processed: 408 average time/residue: 0.6441 time to fit residues: 463.4024 Evaluate side-chains 403 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 272 time to evaluate : 6.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1162 CYS Chi-restraints excluded: chain A residue 1346 SER Chi-restraints excluded: chain A residue 1384 ASN Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1552 VAL Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1829 LEU Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1856 ARG Chi-restraints excluded: chain A residue 1919 LEU Chi-restraints excluded: chain A residue 1931 GLU Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2254 ASP Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2453 TYR Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2544 VAL Chi-restraints excluded: chain A residue 2692 TYR Chi-restraints excluded: chain A residue 2767 CYS Chi-restraints excluded: chain A residue 2795 ILE Chi-restraints excluded: chain A residue 2800 VAL Chi-restraints excluded: chain A residue 2990 CYS Chi-restraints excluded: chain A residue 3020 CYS Chi-restraints excluded: chain A residue 3029 CYS Chi-restraints excluded: chain A residue 3128 CYS Chi-restraints excluded: chain A residue 3136 TYR Chi-restraints excluded: chain A residue 3145 LEU Chi-restraints excluded: chain A residue 3205 PHE Chi-restraints excluded: chain A residue 3232 VAL Chi-restraints excluded: chain A residue 3265 THR Chi-restraints excluded: chain A residue 3269 HIS Chi-restraints excluded: chain A residue 3289 LEU Chi-restraints excluded: chain A residue 3314 VAL Chi-restraints excluded: chain A residue 3315 ASP Chi-restraints excluded: chain A residue 3400 HIS Chi-restraints excluded: chain A residue 3478 CYS Chi-restraints excluded: chain A residue 3520 LEU Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3593 HIS Chi-restraints excluded: chain A residue 3597 GLU Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3729 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3881 PHE Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4268 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 905 ARG Chi-restraints excluded: chain B residue 1291 CYS Chi-restraints excluded: chain B residue 1296 ASP Chi-restraints excluded: chain B residue 1392 ILE Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1560 LEU Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1698 GLN Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1886 LEU Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2167 VAL Chi-restraints excluded: chain B residue 2173 GLU Chi-restraints excluded: chain B residue 2179 THR Chi-restraints excluded: chain B residue 2188 VAL Chi-restraints excluded: chain B residue 2242 MET Chi-restraints excluded: chain B residue 2280 THR Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2713 CYS Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3220 SER Chi-restraints excluded: chain B residue 3256 MET Chi-restraints excluded: chain B residue 3362 ILE Chi-restraints excluded: chain B residue 3417 ILE Chi-restraints excluded: chain B residue 3422 VAL Chi-restraints excluded: chain B residue 3507 ARG Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3553 ARG Chi-restraints excluded: chain B residue 3554 PHE Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3790 SER Chi-restraints excluded: chain B residue 3794 ASP Chi-restraints excluded: chain B residue 3952 VAL Chi-restraints excluded: chain B residue 3982 THR Chi-restraints excluded: chain B residue 4136 VAL Chi-restraints excluded: chain B residue 4261 TYR Chi-restraints excluded: chain B residue 4268 LEU Chi-restraints excluded: chain B residue 4283 GLU Chi-restraints excluded: chain B residue 4312 VAL Chi-restraints excluded: chain B residue 4365 SER Chi-restraints excluded: chain B residue 4375 LEU Chi-restraints excluded: chain I residue 3 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 418 optimal weight: 20.0000 chunk 541 optimal weight: 10.0000 chunk 726 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 629 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 189 optimal weight: 5.9990 chunk 683 optimal weight: 3.9990 chunk 285 optimal weight: 0.5980 chunk 701 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A1312 HIS ** A2702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2959 ASN A3782 GLN ** A3979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.119804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.097224 restraints weight = 222356.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.094221 restraints weight = 333593.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.092942 restraints weight = 278791.980| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 71548 Z= 0.182 Angle : 0.579 16.300 97174 Z= 0.297 Chirality : 0.046 0.432 10764 Planarity : 0.004 0.067 12770 Dihedral : 6.483 60.362 12946 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.86 % Allowed : 17.00 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.09), residues: 8608 helix: -2.88 (0.30), residues: 179 sheet: -0.74 (0.11), residues: 2337 loop : -0.54 (0.08), residues: 6092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A4216 HIS 0.016 0.001 HIS B3402 PHE 0.024 0.001 PHE A4033 TYR 0.020 0.001 TYR B3665 ARG 0.010 0.000 ARG A3094 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13098.75 seconds wall clock time: 231 minutes 54.67 seconds (13914.67 seconds total)